make -k pf02272-tuned-blast.rdb pf02272-tuned-double-blast.rdb make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' make[1]: *** No rule to make target `pf02272-tuned-blast.rdb'. make[1]: *** No rule to make target `pf02272-tuned-double-blast.rdb'. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' make: [pf02272-tuned.blast-all] Error 2 (ignored) make -k pf02272-tuned.t2k.a2m.gz \ pf02272-tuned.t2k.pa \ pf02272-tuned.t2k.pa.html \ pf02272-tuned.t2k.2d \ pf02272-tuned.t2k.tree \ pf02272-tuned.t2k_sorted.pa \ pf02272-tuned.t2k.tree.ps \ pf02272-tuned.t2k.tree-unroot.ps make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' make[1]: *** No rule to make target `pf02272-tuned.t2k.a2m.gz'. make[1]: Target `pf02272-tuned.t2k.pa' not remade because of errors. make[1]: Target `pf02272-tuned.t2k.pa.html' not remade because of errors. make[1]: Target `pf02272-tuned.t2k.2d' not remade because of errors. make[1]: Target `pf02272-tuned.t2k.tree' not remade because of errors. make[1]: Target `pf02272-tuned.t2k_sorted.pa' not remade because of errors. make[1]: Target `pf02272-tuned.t2k.tree.ps' not remade because of errors. make[1]: Target `pf02272-tuned.t2k.tree-unroot.ps' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' make: [pf02272-tuned.align] Error 2 (ignored) make: *** No rule to make target `pf02272-tuned.t2k-logo.eps', needed by `logo'. Stop. make -k pf02272-tuned-blast.rdb pf02272-tuned-double-blast.rdb make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' /projects/compbio/experiments/casp4/scripts/single-blast -q pf02272-tuned.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > pf02272-tuned-blast.rdb starting RECJ_ECOLI/382-451 with E=10 starting RECJ_ERWCH/381-449 with E=10 starting RECJ_HAEIN/376-445 with E=10 starting P73518/390-455 with E=10 starting O32044/370-436 with E=10 starting O83702/514-575 with E=10 starting Q9Z7Z0/390-454 with E=10 starting P94659/317-381 with E=10 starting O84453/389-453 with E=10 starting Q9ZD22/386-452 with E=10 starting Q9ZMA0/338-403 with E=10 starting O67909/370-434 with E=10 starting Y371_MYCGE/252-315 with E=10 starting O51269/507-572 with E=10 starting Q9ZM41/283-342 with E=10 starting O67552/249-312 with E=10 starting O51564/262-322 with E=10 starting O83450/285-343 with E=10 starting P71615/275-333 with E=10 starting MGPA_MYCPN/261-317 with E=10 starting MGPA_MYCGE/296-360 with E=10 starting O31824/247-305 with E=10 starting YG33_METJA/394-461 with E=10 starting O58017/401-472 with E=10 starting O28250/387-458 with E=10 starting Y988_METJA/239-310 with E=10 starting O73979/249-318 with E=10 starting Y977_METJA/396-466 with E=10 starting O26266/371-441 with E=10 starting O57804/392-465 with E=10 starting O29523/379-449 with E=10 starting O27473/379-449 with E=10 starting O29559/362-431 with E=10 starting Y831_METJA/355-424 with E=10 starting YYBT_BACSU/588-647 with E=10 starting O66728/230-290 with E=10 starting O58035/847-912 with E=10 starting SYA_ARCFU/831-899 with E=10 starting O67323/793-863 with E=10 starting SYA_THIFE/800-870 with E=10 starting SYA_ECOLI/799-869 with E=10 starting SYA_BACSU/801-872 with E=10 starting SYA_HAEIN/798-868 with E=10 starting SYA_BARBA/810-882 with E=10 starting SYA_SYNY3/797-870 with E=10 starting Q9ZCA4/802-873 with E=10 starting SYA_METJA/829-887 with E=10 starting Q9Z714/793-865 with E=10 starting O84754/846-917 with E=10 starting O57734/333-400 with E=10 starting SYAC_SCHPO/881-951 with E=10 starting SYAC_YEAST/877-950 with E=10 starting SYA_METTH/817-891 with E=10 starting SYA_THETH/808-882 with E=10 starting SYA_MYCTU/821-895 with E=10 starting O01541/890-961 with E=10 starting SYA_HUMAN/886-957 with E=10 starting SYA_BOMMO/889-960 with E=10 starting SYA_HELPY/772-839 with E=10 starting SYA_ARATH/923-996 with E=10 starting RECJ_ECOLI/382-451 with E=10 starting RECJ_ERWCH/381-449 with E=10 starting RECJ_HAEIN/376-445 with E=10 starting P73518/390-455 with E=10 starting O32044/370-436 with E=10 starting O83702/514-575 with E=10 starting Q9Z7Z0/390-454 with E=10 starting P94659/317-381 with E=10 starting O84453/389-453 with E=10 starting Q9ZD22/386-452 with E=10 starting Q9ZMA0/338-403 with E=10 starting O67909/370-434 with E=10 starting Y371_MYCGE/252-315 with E=10 starting O51269/507-572 with E=10 starting Q9ZM41/283-342 with E=10 starting O67552/249-312 with E=10 starting O51564/262-322 with E=10 starting O83450/285-343 with E=10 starting P71615/275-333 with E=10 starting MGPA_MYCPN/261-317 with E=10 starting MGPA_MYCGE/296-360 with E=10 starting O31824/247-305 with E=10 starting YG33_METJA/394-461 with E=10 starting O58017/401-472 with E=10 starting O28250/387-458 with E=10 starting Y988_METJA/239-310 with E=10 starting O73979/249-318 with E=10 starting Y977_METJA/396-466 with E=10 starting O26266/371-441 with E=10 starting O57804/392-465 with E=10 starting O29523/379-449 with E=10 starting O27473/379-449 with E=10 starting O29559/362-431 with E=10 starting Y831_METJA/355-424 with E=10 starting YYBT_BACSU/588-647 with E=10 starting O66728/230-290 with E=10 starting O58035/847-912 with E=10 starting SYA_ARCFU/831-899 with E=10 starting O67323/793-863 with E=10 starting SYA_THIFE/800-870 with E=10 starting SYA_ECOLI/799-869 with E=10 starting SYA_BACSU/801-872 with E=10 starting SYA_HAEIN/798-868 with E=10 starting SYA_BARBA/810-882 with E=10 starting SYA_SYNY3/797-870 with E=10 starting Q9ZCA4/802-873 with E=10 starting SYA_METJA/829-887 with E=10 starting Q9Z714/793-865 with E=10 starting O84754/846-917 with E=10 starting O57734/333-400 with E=10 starting SYAC_SCHPO/881-951 with E=10 starting SYAC_YEAST/877-950 with E=10 starting SYA_METTH/817-891 with E=10 starting SYA_THETH/808-882 with E=10 starting SYA_MYCTU/821-895 with E=10 starting O01541/890-961 with E=10 starting SYA_HUMAN/886-957 with E=10 starting SYA_BOMMO/889-960 with E=10 starting SYA_HELPY/772-839 with E=10 starting SYA_ARATH/923-996 with E=10 /projects/compbio/experiments/casp4/scripts/double-blast -q pf02272-tuned.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > pf02272-tuned-double-blast.rdb starting RECJ_ECOLI/382-451 with E=0.000050 RECJ_ECOLI/382-451 RECJ_ECOLI/382-451 blasting: RECJ_ECOLI/382-451 gi|96357|pir||C39202_383:450 blasting: RECJ_ECOLI/382-451 gi|2507106|sp|P21893|RECJ_ECOLI_382:449 blasting: RECJ_ECOLI/382-451 gi|1172895|sp|P45112|RECJ_HAEIN_376:443 blasting: RECJ_ECOLI/382-451 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_ECOLI/382-451 gi|7226077|gb|AAF41253.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|7228156|emb|CAB77039.1|_381:450 blasting: RECJ_ECOLI/382-451 gi|7379749|emb|CAB84317.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|7453624|gb|AAF62912.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|9106065|gb|AAF83920.1|AE003946_11_370:439 blasting: RECJ_ECOLI/382-451 gi|9656991|gb|AAF95560.1|_385:452 blasting: starting RECJ_ERWCH/381-449 with E=0.000050 RECJ_ERWCH/381-449 RECJ_ERWCH/381-449 blasting: RECJ_ERWCH/381-449 gi|96357|pir||C39202_383:450 blasting: RECJ_ERWCH/381-449 gi|2507106|sp|P21893|RECJ_ECOLI_382:449 blasting: RECJ_ERWCH/381-449 gi|1172895|sp|P45112|RECJ_HAEIN_376:443 blasting: RECJ_ERWCH/381-449 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_ERWCH/381-449 gi|7226077|gb|AAF41253.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|7228156|emb|CAB77039.1|_381:438 blasting: RECJ_ERWCH/381-449 gi|7379749|emb|CAB84317.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|7453624|gb|AAF62912.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|9106065|gb|AAF83920.1|AE003946_11_370:427 blasting: RECJ_ERWCH/381-449 gi|9656991|gb|AAF95560.1|_385:452 blasting: starting RECJ_HAEIN/376-445 with E=0.000050 RECJ_HAEIN/376-445 RECJ_HAEIN/376-445 blasting: RECJ_HAEIN/376-445 gi|96357|pir||C39202_383:452 blasting: RECJ_HAEIN/376-445 gi|2507106|sp|P21893|RECJ_ECOLI_382:451 blasting: RECJ_HAEIN/376-445 gi|1172895|sp|P45112|RECJ_HAEIN_376:445 blasting: RECJ_HAEIN/376-445 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_HAEIN/376-445 gi|7226077|gb|AAF41253.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|7228156|emb|CAB77039.1|_381:450 blasting: RECJ_HAEIN/376-445 gi|7379749|emb|CAB84317.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|7453624|gb|AAF62912.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|9106065|gb|AAF83920.1|AE003946_11_370:439 blasting: RECJ_HAEIN/376-445 gi|9656991|gb|AAF95560.1|_385:454 blasting: starting P73518/390-455 with E=0.000050 P73518/390-455 P73518/390-455 blasting: P73518/390-455 gi|7470865|pir||S77224_391:454 blasting: starting O32044/370-436 with E=0.000050 O32044/370-436 O32044/370-436 blasting: O32044/370-436 gi|7475820|pir||H69980_371:436 blasting: starting O83702/514-575 with E=0.000050 O83702/514-575 O83702/514-575 blasting: O83702/514-575 gi|7521421|pir||D71289_515:575 blasting: starting Q9Z7Z0/390-454 with E=0.000050 Q9Z7Z0/390-454 Q9Z7Z0/390-454 blasting: Q9Z7Z0/390-454 gi|2126389|pir||PC4257_67:129 blasting: Q9Z7Z0/390-454 gi|3063673|gb|AAC14136.1|_318:380 blasting: Q9Z7Z0/390-454 gi|7451688|pir||H71513_390:452 blasting: Q9Z7Z0/390-454 gi|7451687|pir||D72062_391:453 blasting: Q9Z7Z0/390-454 gi|7190761|gb|AAF39542.1|_390:452 blasting: starting P94659/317-381 with E=0.000050 P94659/317-381 P94659/317-381 blasting: P94659/317-381 gi|2126389|pir||PC4257_68:129 blasting: P94659/317-381 gi|3063673|gb|AAC14136.1|_319:380 blasting: P94659/317-381 gi|7451688|pir||H71513_391:452 blasting: P94659/317-381 gi|7451687|pir||D72062_392:453 blasting: P94659/317-381 gi|7190761|gb|AAF39542.1|_391:452 blasting: starting O84453/389-453 with E=0.000050 O84453/389-453 O84453/389-453 blasting: O84453/389-453 gi|2126389|pir||PC4257_67:129 blasting: O84453/389-453 gi|3063673|gb|AAC14136.1|_318:380 blasting: O84453/389-453 gi|7451688|pir||H71513_390:452 blasting: O84453/389-453 gi|7451687|pir||D72062_391:453 blasting: O84453/389-453 gi|7190761|gb|AAF39542.1|_390:452 blasting: starting Q9ZD22/386-452 with E=0.000050 Q9ZD22/386-452 Q9ZD22/386-452 blasting: Q9ZD22/386-452 gi|7451686|pir||G71656_386:452 blasting: starting Q9ZMA0/338-403 with E=0.000050 Q9ZMA0/338-403 Q9ZMA0/338-403 blasting: Q9ZMA0/338-403 gi|7451683|pir||D64563_338:403 blasting: Q9ZMA0/338-403 gi|7451682|pir||B71946_338:403 blasting: starting O67909/370-434 with E=0.000050 O67909/370-434 O67909/370-434 blasting: O67909/370-434 gi|7451685|pir||A70485_370:434 blasting: starting Y371_MYCGE/252-315 with E=0.000050 Y371_MYCGE/252-315 Y371_MYCGE/252-315 blasting: Y371_MYCGE/252-315 gi|2496409|sp|Q49428|Y371_MYCGE_252:315 blasting: Y371_MYCGE/252-315 gi|2496410|sp|P75229|Y371_MYCPN_252:315 blasting: starting O51269/507-572 with E=0.000050 O51269/507-572 O51269/507-572 blasting: O51269/507-572 gi|7463775|pir||F70131_510:572 blasting: starting Q9ZM41/283-342 with E=0.000050 Q9ZM41/283-342 Q9ZM41/283-342 blasting: Q9ZM41/283-342 gi|7464457|pir||B64650_287:327 blasting: Q9ZM41/283-342 gi|7464457|pir||B64650_328:343 blasting: Q9ZM41/283-342 gi|7464707|pir||D71937_286:326 blasting: Q9ZM41/283-342 gi|7464707|pir||D71937_327:342 blasting: starting O67552/249-312 with E=0.000050 O67552/249-312 O67552/249-312 blasting: O67552/249-312 gi|7445472|pir||F70440_249:312 blasting: starting O51564/262-322 with E=0.000050 O51564/262-322 O51564/262-322 blasting: O51564/262-322 gi|7430137|pir||B70177_264:322 blasting: starting O83450/285-343 with E=0.000050 O83450/285-343 O83450/285-343 blasting: O83450/285-343 gi|7514584|pir||D71323_286:341 blasting: starting P71615/275-333 with E=0.000050 P71615/275-333 P71615/275-333 blasting: P71615/275-333 gi|7477397|pir||H70693_278:328 blasting: starting MGPA_MYCPN/261-317 with E=0.000050 MGPA_MYCPN/261-317 MGPA_MYCPN/261-317 blasting: MGPA_MYCPN/261-317 gi|80890|pir||JQ0091_190:239 blasting: MGPA_MYCPN/261-317 gi|80899|pir||JS0068_179:228 blasting: MGPA_MYCPN/261-317 gi|80899|pir||JS0068_200:234 blasting: MGPA_MYCPN/261-317 gi|1346531|sp|P22746|MGPA_MYCGE_298:347 blasting: MGPA_MYCPN/261-317 gi|2498554|sp|P75144|MGPA_MYCPN_262:311 blasting: MGPA_MYCPN/261-317 gi|2498554|sp|P75144|MGPA_MYCPN_283:317 blasting: starting MGPA_MYCGE/296-360 with E=0.000050 MGPA_MYCGE/296-360 MGPA_MYCGE/296-360 blasting: MGPA_MYCGE/296-360 gi|80890|pir||JQ0091_190:252 blasting: MGPA_MYCGE/296-360 gi|80899|pir||JS0068_179:239 blasting: MGPA_MYCGE/296-360 gi|1346531|sp|P22746|MGPA_MYCGE_298:360 blasting: MGPA_MYCGE/296-360 gi|2498554|sp|P75144|MGPA_MYCPN_262:322 blasting: starting O31824/247-305 with E=0.000050 O31824/247-305 O31824/247-305 blasting: O31824/247-305 gi|7475203|pir||A69893_259:305 blasting: O31824/247-305 gi|7475203|pir||A69893_247:258 blasting: starting YG33_METJA/394-461 with E=0.000050 YG33_METJA/394-461 YG33_METJA/394-461 blasting: YG33_METJA/394-461 gi|3025197|sp|Q59027|YG33_METJA_397:442 blasting: YG33_METJA/394-461 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: YG33_METJA/394-461 gi|7448978|pir||D69503_392:439 blasting: YG33_METJA/394-461 gi|7448978|pir||D69503_440:458 blasting: YG33_METJA/394-461 gi|7448980|pir||H71452_406:453 blasting: YG33_METJA/394-461 gi|7448980|pir||H71452_454:472 blasting: YG33_METJA/394-461 gi|7448979|pir||B75216_406:453 blasting: YG33_METJA/394-461 gi|7448979|pir||B75216_454:472 blasting: starting O58017/401-472 with E=0.000050 O58017/401-472 O58017/401-472 blasting: O58017/401-472 gi|3025197|sp|Q59027|YG33_METJA_396:442 blasting: O58017/401-472 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: O58017/401-472 gi|7448978|pir||D69503_389:439 blasting: O58017/401-472 gi|7448978|pir||D69503_440:458 blasting: O58017/401-472 gi|7448980|pir||H71452_403:453 blasting: O58017/401-472 gi|7448980|pir||H71452_454:472 blasting: O58017/401-472 gi|7448979|pir||B75216_403:453 blasting: O58017/401-472 gi|7448979|pir||B75216_454:472 blasting: starting O28250/387-458 with E=0.000050 O28250/387-458 O28250/387-458 blasting: O28250/387-458 gi|3025197|sp|Q59027|YG33_METJA_396:442 blasting: O28250/387-458 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: O28250/387-458 gi|7448978|pir||D69503_389:439 blasting: O28250/387-458 gi|7448978|pir||D69503_440:458 blasting: O28250/387-458 gi|7448980|pir||H71452_403:453 blasting: O28250/387-458 gi|7448980|pir||H71452_454:472 blasting: O28250/387-458 gi|7448979|pir||B75216_403:453 blasting: O28250/387-458 gi|7448979|pir||B75216_454:472 blasting: starting Y988_METJA/239-310 with E=0.000050 Y988_METJA/239-310 Y988_METJA/239-310 blasting: Y988_METJA/239-310 gi|3024962|sp|Q58395|Y988_METJA_241:297 blasting: Y988_METJA/239-310 gi|3024962|sp|Q58395|Y988_METJA_298:310 blasting: Y988_METJA/239-310 gi|7518694|pir||B71167_251:303 blasting: Y988_METJA/239-310 gi|7518105|pir||C75065_252:304 blasting: starting O73979/249-318 with E=0.000050 O73979/249-318 O73979/249-318 blasting: O73979/249-318 gi|3024962|sp|Q58395|Y988_METJA_246:295 blasting: O73979/249-318 gi|7450700|pir||B69086_377:425 blasting: O73979/249-318 gi|7450705|pir||G69341_383:433 blasting: O73979/249-318 gi|7518694|pir||B71167_252:318 blasting: O73979/249-318 gi|7518105|pir||C75065_253:319 blasting: starting Y977_METJA/396-466 with E=0.000050 Y977_METJA/396-466 Y977_METJA/396-466 blasting: Y977_METJA/396-466 gi|2842584|sp|Q58387|RECJ_METJA_399:466 blasting: Y977_METJA/396-466 gi|7450700|pir||B69086_374:437 blasting: Y977_METJA/396-466 gi|7450705|pir||G69341_382:445 blasting: Y977_METJA/396-466 gi|7450702|pir||C69337_371:427 blasting: starting O26266/371-441 with E=0.000050 O26266/371-441 O26266/371-441 blasting: O26266/371-441 gi|2842584|sp|Q58387|RECJ_METJA_404:465 blasting: O26266/371-441 gi|7450700|pir||B69086_371:440 blasting: O26266/371-441 gi|7450705|pir||G69341_387:448 blasting: O26266/371-441 gi|7450702|pir||C69337_376:430 blasting: O26266/371-441 gi|7450704|pir||H71224_408:464 blasting: O26266/371-441 gi|7518694|pir||B71167_259:302 blasting: O26266/371-441 gi|7450703|pir||G75192_409:465 blasting: O26266/371-441 gi|7518105|pir||C75065_260:303 blasting: starting O57804/392-465 with E=0.000050 O57804/392-465 O57804/392-465 blasting: O57804/392-465 gi|7450700|pir||B69086_372:440 blasting: O57804/392-465 gi|7450701|pir||E69056_392:448 blasting: O57804/392-465 gi|7450705|pir||G69341_380:448 blasting: O57804/392-465 gi|7450702|pir||C69337_363:430 blasting: O57804/392-465 gi|7450704|pir||H71224_393:464 blasting: O57804/392-465 gi|7450703|pir||G75192_394:465 blasting: starting O29523/379-449 with E=0.000050 O29523/379-449 O29523/379-449 blasting: O29523/379-449 gi|2833617|sp|Q58241|Y831_METJA_355:423 blasting: O29523/379-449 gi|2842584|sp|Q58387|RECJ_METJA_397:465 blasting: O29523/379-449 gi|7450700|pir||B69086_372:440 blasting: O29523/379-449 gi|7450701|pir||E69056_389:448 blasting: O29523/379-449 gi|7450705|pir||G69341_379:448 blasting: O29523/379-449 gi|7450702|pir||C69337_362:430 blasting: O29523/379-449 gi|7450704|pir||H71224_392:464 blasting: O29523/379-449 gi|7518694|pir||B71167_256:315 blasting: O29523/379-449 gi|7450703|pir||G75192_393:465 blasting: O29523/379-449 gi|7518105|pir||C75065_257:316 blasting: starting O27473/379-449 with E=0.000050 O27473/379-449 O27473/379-449 blasting: O27473/379-449 gi|2833617|sp|Q58241|Y831_METJA_369:424 blasting: O27473/379-449 gi|7450700|pir||B69086_374:440 blasting: O27473/379-449 gi|7450701|pir||E69056_382:449 blasting: O27473/379-449 gi|7450705|pir||G69341_382:448 blasting: O27473/379-449 gi|7450702|pir||C69337_365:430 blasting: O27473/379-449 gi|7450704|pir||H71224_408:465 blasting: O27473/379-449 gi|7450703|pir||G75192_409:466 blasting: starting O29559/362-431 with E=0.000050 O29559/362-431 O29559/362-431 blasting: O29559/362-431 gi|2833617|sp|Q58241|Y831_METJA_355:423 blasting: O29559/362-431 gi|2842584|sp|Q58387|RECJ_METJA_406:465 blasting: O29559/362-431 gi|7450705|pir||G69341_379:448 blasting: O29559/362-431 gi|7450702|pir||C69337_362:430 blasting: starting Y831_METJA/355-424 with E=0.000050 Y831_METJA/355-424 Y831_METJA/355-424 blasting: Y831_METJA/355-424 gi|2833617|sp|Q58241|Y831_METJA_355:424 blasting: Y831_METJA/355-424 gi|7450701|pir||E69056_393:449 blasting: Y831_METJA/355-424 gi|7450705|pir||G69341_379:448 blasting: Y831_METJA/355-424 gi|7450702|pir||C69337_362:430 blasting: starting YYBT_BACSU/588-647 with E=0.000050 YYBT_BACSU/588-647 YYBT_BACSU/588-647 blasting: YYBT_BACSU/588-647 gi|586814|sp|P37484|YYBT_BACSU_588:646 blasting: starting O66728/230-290 with E=0.000050 O66728/230-290 O66728/230-290 blasting: O66728/230-290 gi|7520820|pir||D70337_233:284 blasting: starting O58035/847-912 with E=0.000050 O58035/847-912 O58035/847-912 blasting: O58035/847-912 gi|6707751|sp|O58035|SYA_PYRHO_849:912 blasting: O58035/847-912 gi|7437620|pir||B75017_849:908 blasting: starting SYA_ARCFU/831-899 with E=0.000050 SYA_ARCFU/831-899 SYA_ARCFU/831-899 blasting: SYA_ARCFU/831-899 gi|3334348|sp|O28029|SYA_ARCFU_831:898 blasting: starting O67323/793-863 with E=0.000050 O67323/793-863 O67323/793-863 blasting: O67323/793-863 gi|145220|gb|AAA03208.1|_801:868 blasting: O67323/793-863 gi|1174496|sp|P43815|SYA_HAEIN_800:868 blasting: O67323/793-863 gi|2500957|sp|P70865|SYA_BARBA_813:882 blasting: O67323/793-863 gi|2507425|sp|P00957|SYA_ECOLI_801:868 blasting: O67323/793-863 gi|2281029|dbj|BAA21554.1|_3:70 blasting: O67323/793-863 gi|3122886|sp|O34526|SYA_BACSU_803:872 blasting: O67323/793-863 gi|6226165|sp|O67323|SYA_AQUAE_795:863 blasting: O67323/793-863 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:863 blasting: O67323/793-863 gi|6707752|sp|Q9X1B6|SYA_THEMA_792:860 blasting: O67323/793-863 gi|7226845|gb|AAF41948.1|_799:867 blasting: starting SYA_THIFE/800-870 with E=0.000050 SYA_THIFE/800-870 SYA_THIFE/800-870 blasting: SYA_THIFE/800-870 gi|145220|gb|AAA03208.1|_802:864 blasting: SYA_THIFE/800-870 gi|1174496|sp|P43815|SYA_HAEIN_801:852 blasting: SYA_THIFE/800-870 gi|2500961|sp|Q56273|SYA_THIFE_803:870 blasting: SYA_THIFE/800-870 gi|2507425|sp|P00957|SYA_ECOLI_802:864 blasting: SYA_THIFE/800-870 gi|2281029|dbj|BAA21554.1|_4:66 blasting: SYA_THIFE/800-870 gi|3122886|sp|O34526|SYA_BACSU_804:867 blasting: SYA_THIFE/800-870 gi|3293580|gb|AAC25784.1|_1:54 blasting: SYA_THIFE/800-870 gi|7226845|gb|AAF41948.1|_800:864 blasting: SYA_THIFE/800-870 gi|7380429|emb|CAB85015.1|_800:862 blasting: SYA_THIFE/800-870 gi|9104908|gb|AAF82937.1|AE003866_2_841:905 blasting: SYA_THIFE/800-870 gi|9654973|gb|AAF93713.1|_787:851 blasting: starting SYA_ECOLI/799-869 with E=0.000050 SYA_ECOLI/799-869 SYA_ECOLI/799-869 blasting: SYA_ECOLI/799-869 gi|145220|gb|AAA03208.1|_801:869 blasting: SYA_ECOLI/799-869 gi|1174496|sp|P43815|SYA_HAEIN_800:854 blasting: SYA_ECOLI/799-869 gi|2500961|sp|Q56273|SYA_THIFE_802:864 blasting: SYA_ECOLI/799-869 gi|2500957|sp|P70865|SYA_BARBA_812:869 blasting: SYA_ECOLI/799-869 gi|2500959|sp|P74423|SYA_SYNY3_800:864 blasting: SYA_ECOLI/799-869 gi|2507425|sp|P00957|SYA_ECOLI_801:869 blasting: SYA_ECOLI/799-869 gi|2281029|dbj|BAA21554.1|_3:71 blasting: SYA_ECOLI/799-869 gi|3122886|sp|O34526|SYA_BACSU_803:866 blasting: SYA_ECOLI/799-869 gi|6226165|sp|O67323|SYA_AQUAE_795:857 blasting: SYA_ECOLI/799-869 gi|3293580|gb|AAC25784.1|_1:51 blasting: SYA_ECOLI/799-869 gi|5834358|gb|AAD53924.1|AF179611_8_814:868 blasting: SYA_ECOLI/799-869 gi|7471091|pir||F75289_828:885 blasting: SYA_ECOLI/799-869 gi|6967975|emb|CAB75143.1|_771:830 blasting: SYA_ECOLI/799-869 gi|7226845|gb|AAF41948.1|_799:860 blasting: SYA_ECOLI/799-869 gi|7380429|emb|CAB85015.1|_799:859 blasting: SYA_ECOLI/799-869 gi|7404473|sp|P27866|SYA_RHIME_822:870 blasting: SYA_ECOLI/799-869 gi|8249960|emb|CAB93381.1|_814:874 blasting: SYA_ECOLI/799-869 gi|9104908|gb|AAF82937.1|AE003866_2_840:903 blasting: SYA_ECOLI/799-869 gi|9654973|gb|AAF93713.1|_786:848 blasting: starting SYA_BACSU/801-872 with E=0.000050 SYA_BACSU/801-872 SYA_BACSU/801-872 blasting: SYA_BACSU/801-872 gi|135089|sp|P21894|SYA_BOMMO_900:955 blasting: SYA_BACSU/801-872 gi|145220|gb|AAA03208.1|_801:864 blasting: SYA_BACSU/801-872 gi|1174496|sp|P43815|SYA_HAEIN_800:863 blasting: SYA_BACSU/801-872 gi|2500961|sp|Q56273|SYA_THIFE_802:865 blasting: SYA_BACSU/801-872 gi|2500957|sp|P70865|SYA_BARBA_812:877 blasting: SYA_BACSU/801-872 gi|2500959|sp|P74423|SYA_SYNY3_800:865 blasting: SYA_BACSU/801-872 gi|2507425|sp|P00957|SYA_ECOLI_801:864 blasting: SYA_BACSU/801-872 gi|2281029|dbj|BAA21554.1|_3:66 blasting: SYA_BACSU/801-872 gi|3334347|sp|O27718|SYA_METTH_830:886 blasting: SYA_BACSU/801-872 gi|3122886|sp|O34526|SYA_BACSU_803:872 blasting: SYA_BACSU/801-872 gi|7450705|pir||G69341_382:441 blasting: SYA_BACSU/801-872 gi|6226165|sp|O67323|SYA_AQUAE_795:858 blasting: SYA_BACSU/801-872 gi|7518694|pir||B71167_251:312 blasting: SYA_BACSU/801-872 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_BACSU/801-872 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:858 blasting: SYA_BACSU/801-872 gi|6707752|sp|Q9X1B6|SYA_THEMA_792:855 blasting: SYA_BACSU/801-872 gi|7518105|pir||C75065_252:313 blasting: SYA_BACSU/801-872 gi|5834358|gb|AAD53924.1|AF179611_8_814:878 blasting: SYA_BACSU/801-872 gi|7471091|pir||F75289_826:875 blasting: SYA_BACSU/801-872 gi|6967975|emb|CAB75143.1|_771:831 blasting: SYA_BACSU/801-872 gi|7226845|gb|AAF41948.1|_799:862 blasting: SYA_BACSU/801-872 gi|7380429|emb|CAB85015.1|_799:862 blasting: SYA_BACSU/801-872 gi|7404473|sp|P27866|SYA_RHIME_814:878 blasting: SYA_BACSU/801-872 gi|8249960|emb|CAB93381.1|_814:878 blasting: SYA_BACSU/801-872 gi|9654973|gb|AAF93713.1|_786:849 blasting: starting SYA_HAEIN/798-868 with E=0.000050 SYA_HAEIN/798-868 SYA_HAEIN/798-868 blasting: SYA_HAEIN/798-868 gi|145220|gb|AAA03208.1|_802:864 blasting: SYA_HAEIN/798-868 gi|1174496|sp|P43815|SYA_HAEIN_801:866 blasting: SYA_HAEIN/798-868 gi|2500961|sp|Q56273|SYA_THIFE_803:868 blasting: SYA_HAEIN/798-868 gi|2500957|sp|P70865|SYA_BARBA_813:877 blasting: SYA_HAEIN/798-868 gi|2507425|sp|P00957|SYA_ECOLI_802:864 blasting: SYA_HAEIN/798-868 gi|2281029|dbj|BAA21554.1|_4:66 blasting: SYA_HAEIN/798-868 gi|3024653|sp|P56452|SYA_HELPY_782:837 blasting: SYA_HAEIN/798-868 gi|3122886|sp|O34526|SYA_BACSU_804:867 blasting: SYA_HAEIN/798-868 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_HAEIN/798-868 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_782:837 blasting: SYA_HAEIN/798-868 gi|5834358|gb|AAD53924.1|AF179611_8_815:879 blasting: SYA_HAEIN/798-868 gi|6967975|emb|CAB75143.1|_772:832 blasting: SYA_HAEIN/798-868 gi|7226845|gb|AAF41948.1|_800:858 blasting: SYA_HAEIN/798-868 gi|7380429|emb|CAB85015.1|_800:853 blasting: SYA_HAEIN/798-868 gi|7404473|sp|P27866|SYA_RHIME_814:879 blasting: SYA_HAEIN/798-868 gi|9654973|gb|AAF93713.1|_787:850 blasting: starting SYA_BARBA/810-882 with E=0.000050 SYA_BARBA/810-882 SYA_BARBA/810-882 blasting: SYA_BARBA/810-882 gi|145220|gb|AAA03208.1|_801:866 blasting: SYA_BARBA/810-882 gi|1174496|sp|P43815|SYA_HAEIN_800:863 blasting: SYA_BARBA/810-882 gi|2500957|sp|P70865|SYA_BARBA_812:882 blasting: SYA_BARBA/810-882 gi|2507425|sp|P00957|SYA_ECOLI_801:866 blasting: SYA_BARBA/810-882 gi|2281029|dbj|BAA21554.1|_3:68 blasting: SYA_BARBA/810-882 gi|6226165|sp|O67323|SYA_AQUAE_795:858 blasting: SYA_BARBA/810-882 gi|5834358|gb|AAD53924.1|AF179611_8_814:880 blasting: SYA_BARBA/810-882 gi|7380429|emb|CAB85015.1|_799:864 blasting: SYA_BARBA/810-882 gi|7404473|sp|P27866|SYA_RHIME_813:880 blasting: SYA_BARBA/810-882 gi|9654973|gb|AAF93713.1|_786:849 blasting: starting SYA_SYNY3/797-870 with E=0.000050 SYA_SYNY3/797-870 SYA_SYNY3/797-870 blasting: SYA_SYNY3/797-870 gi|145220|gb|AAA03208.1|_802:866 blasting: SYA_SYNY3/797-870 gi|1174496|sp|P43815|SYA_HAEIN_801:866 blasting: SYA_SYNY3/797-870 gi|2500961|sp|Q56273|SYA_THIFE_803:868 blasting: SYA_SYNY3/797-870 gi|2500959|sp|P74423|SYA_SYNY3_799:868 blasting: SYA_SYNY3/797-870 gi|2507425|sp|P00957|SYA_ECOLI_802:866 blasting: SYA_SYNY3/797-870 gi|2281029|dbj|BAA21554.1|_4:68 blasting: SYA_SYNY3/797-870 gi|3334347|sp|O27718|SYA_METTH_825:889 blasting: SYA_SYNY3/797-870 gi|3122886|sp|O34526|SYA_BACSU_802:869 blasting: SYA_SYNY3/797-870 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_SYNY3/797-870 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:858 blasting: SYA_SYNY3/797-870 gi|6967975|emb|CAB75143.1|_770:831 blasting: SYA_SYNY3/797-870 gi|7226845|gb|AAF41948.1|_798:862 blasting: SYA_SYNY3/797-870 gi|7380429|emb|CAB85015.1|_798:864 blasting: SYA_SYNY3/797-870 gi|8249960|emb|CAB93381.1|_813:878 blasting: SYA_SYNY3/797-870 gi|9654973|gb|AAF93713.1|_787:849 blasting: starting Q9ZCA4/802-873 with E=0.000050 Q9ZCA4/802-873 Q9ZCA4/802-873 blasting: Q9ZCA4/802-873 gi|6226166|sp|Q9ZCA4|SYA_RICPR_803:872 blasting: starting SYA_METJA/829-887 with E=0.000050 SYA_METJA/829-887 SYA_METJA/829-887 blasting: SYA_METJA/829-887 gi|2500963|sp|Q57984|SYA_METJA_831:887 blasting: starting Q9Z714/793-865 with E=0.000050 Q9Z714/793-865 Q9Z714/793-865 blasting: Q9Z714/793-865 gi|6707750|sp|Q9Z714|SYA_CHLPN_795:865 blasting: Q9Z714/793-865 gi|6707747|sp|O84754|SYA_CHLTR_799:868 blasting: Q9Z714/793-865 gi|7190160|gb|AAF39003.1|_799:868 blasting: Q9Z714/793-865 gi|7437632|pir||E71476_848:917 blasting: starting O84754/846-917 with E=0.000050 O84754/846-917 O84754/846-917 blasting: O84754/846-917 gi|6707750|sp|Q9Z714|SYA_CHLPN_796:863 blasting: O84754/846-917 gi|6707747|sp|O84754|SYA_CHLTR_799:867 blasting: O84754/846-917 gi|7190160|gb|AAF39003.1|_799:867 blasting: O84754/846-917 gi|7437632|pir||E71476_848:916 blasting: starting O57734/333-400 with E=0.000050 O57734/333-400 O57734/333-400 blasting: O57734/333-400 gi|7514241|pir||A71213_340:400 blasting: O57734/333-400 gi|7514241|pir||A71213_333:339 blasting: O57734/333-400 gi|7514245|pir||G75027_341:400 blasting: starting SYAC_SCHPO/881-951 with E=0.000050 SYAC_SCHPO/881-951 SYAC_SCHPO/881-951 blasting: SYAC_SCHPO/881-951 gi|609338|gb|AAC49007.1|_877:947 blasting: SYAC_SCHPO/881-951 gi|3183171|sp|O13914|SYAC_SCHPO_881:951 blasting: starting SYAC_YEAST/877-950 with E=0.000050 SYAC_YEAST/877-950 SYAC_YEAST/877-950 blasting: SYAC_YEAST/877-950 gi|609338|gb|AAC49007.1|_877:947 blasting: SYAC_YEAST/877-950 gi|3183171|sp|O13914|SYAC_SCHPO_881:948 blasting: starting SYA_METTH/817-891 with E=0.000050 SYA_METTH/817-891 SYA_METTH/817-891 blasting: SYA_METTH/817-891 gi|2500959|sp|P74423|SYA_SYNY3_799:865 blasting: SYA_METTH/817-891 gi|3334347|sp|O27718|SYA_METTH_817:888 blasting: SYA_METTH/817-891 gi|3122886|sp|O34526|SYA_BACSU_811:867 blasting: SYA_METTH/817-891 gi|6226165|sp|O67323|SYA_AQUAE_794:859 blasting: SYA_METTH/817-891 gi|6707748|sp|Q9XDM3|SYA_AQUPY_794:859 blasting: SYA_METTH/817-891 gi|6176442|gb|AAF05593.1|AF188718_1_904:955 blasting: SYA_METTH/817-891 gi|7297398|gb|AAF52657.1|_904:955 blasting: starting SYA_THETH/808-882 with E=0.000050 SYA_THETH/808-882 SYA_THETH/808-882 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_830:882 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_808:829 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_478:492 blasting: starting SYA_MYCTU/821-895 with E=0.000050 SYA_MYCTU/821-895 SYA_MYCTU/821-895 blasting: SYA_MYCTU/821-895 gi|3122879|sp|O07438|SYA_MYCTU_821:895 blasting: SYA_MYCTU/821-895 gi|8249960|emb|CAB93381.1|_813:879 blasting: starting O01541/890-961 with E=0.000050 O01541/890-961 O01541/890-961 blasting: O01541/890-961 gi|135089|sp|P21894|SYA_BOMMO_891:958 blasting: O01541/890-961 gi|7500106|pir||T29466_891:959 blasting: O01541/890-961 gi|3024653|sp|P56452|SYA_HELPY_791:837 blasting: O01541/890-961 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_796:837 blasting: O01541/890-961 gi|6176440|gb|AAF05592.1|AF188717_1_870:936 blasting: O01541/890-961 gi|6176442|gb|AAF05593.1|AF188718_1_890:957 blasting: O01541/890-961 gi|7297398|gb|AAF52657.1|_890:957 blasting: starting SYA_HUMAN/886-957 with E=0.000050 SYA_HUMAN/886-957 SYA_HUMAN/886-957 blasting: SYA_HUMAN/886-957 gi|135089|sp|P21894|SYA_BOMMO_890:957 blasting: SYA_HUMAN/886-957 gi|7500106|pir||T29466_892:958 blasting: SYA_HUMAN/886-957 gi|3024653|sp|P56452|SYA_HELPY_775:836 blasting: SYA_HUMAN/886-957 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_775:836 blasting: SYA_HUMAN/886-957 gi|6176440|gb|AAF05592.1|AF188717_1_871:936 blasting: SYA_HUMAN/886-957 gi|6176442|gb|AAF05593.1|AF188718_1_889:956 blasting: SYA_HUMAN/886-957 gi|7297398|gb|AAF52657.1|_889:956 blasting: starting SYA_BOMMO/889-960 with E=0.000050 SYA_BOMMO/889-960 SYA_BOMMO/889-960 blasting: SYA_BOMMO/889-960 gi|135089|sp|P21894|SYA_BOMMO_890:960 blasting: SYA_BOMMO/889-960 gi|7500106|pir||T29466_892:961 blasting: SYA_BOMMO/889-960 gi|3122886|sp|O34526|SYA_BACSU_812:867 blasting: SYA_BOMMO/889-960 gi|6176440|gb|AAF05592.1|AF188717_1_871:941 blasting: SYA_BOMMO/889-960 gi|6176442|gb|AAF05593.1|AF188718_1_889:959 blasting: SYA_BOMMO/889-960 gi|7297398|gb|AAF52657.1|_889:959 blasting: starting SYA_HELPY/772-839 with E=0.000050 SYA_HELPY/772-839 SYA_HELPY/772-839 blasting: SYA_HELPY/772-839 gi|3024653|sp|P56452|SYA_HELPY_775:839 blasting: SYA_HELPY/772-839 gi|3293580|gb|AAC25784.1|_14:53 blasting: SYA_HELPY/772-839 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_775:839 blasting: SYA_HELPY/772-839 gi|6967975|emb|CAB75143.1|_773:831 blasting: starting SYA_ARATH/923-996 with E=0.000050 SYA_ARATH/923-996 SYA_ARATH/923-996 blasting: SYA_ARATH/923-996 gi|421855|pir||S32671_910:979 blasting: SYA_ARATH/923-996 gi|2507426|sp|P36428|SYA_ARATH_924:993 blasting: SYA_ARATH/923-996 gi|1673366|emb|CAA80381.1|_876:945 blasting: SYA_ARATH/923-996 gi|2065021|emb|CAA73145.1|_172:241 blasting: SYA_ARATH/923-996 gi|5734779|gb|AAD50044.1|AC007980_9_876:945 blasting: starting RECJ_ECOLI/382-451 with E=0.000050 RECJ_ECOLI/382-451 RECJ_ECOLI/382-451 blasting: RECJ_ECOLI/382-451 gi|96357|pir||C39202_383:450 blasting: RECJ_ECOLI/382-451 gi|2507106|sp|P21893|RECJ_ECOLI_382:449 blasting: RECJ_ECOLI/382-451 gi|1172895|sp|P45112|RECJ_HAEIN_376:443 blasting: RECJ_ECOLI/382-451 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_ECOLI/382-451 gi|7226077|gb|AAF41253.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|7228156|emb|CAB77039.1|_381:450 blasting: RECJ_ECOLI/382-451 gi|7379749|emb|CAB84317.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|7453624|gb|AAF62912.1|_377:444 blasting: RECJ_ECOLI/382-451 gi|9106065|gb|AAF83920.1|AE003946_11_370:439 blasting: RECJ_ECOLI/382-451 gi|9656991|gb|AAF95560.1|_385:452 blasting: starting RECJ_ERWCH/381-449 with E=0.000050 RECJ_ERWCH/381-449 RECJ_ERWCH/381-449 blasting: RECJ_ERWCH/381-449 gi|96357|pir||C39202_383:450 blasting: RECJ_ERWCH/381-449 gi|2507106|sp|P21893|RECJ_ECOLI_382:449 blasting: RECJ_ERWCH/381-449 gi|1172895|sp|P45112|RECJ_HAEIN_376:443 blasting: RECJ_ERWCH/381-449 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_ERWCH/381-449 gi|7226077|gb|AAF41253.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|7228156|emb|CAB77039.1|_381:438 blasting: RECJ_ERWCH/381-449 gi|7379749|emb|CAB84317.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|7453624|gb|AAF62912.1|_377:434 blasting: RECJ_ERWCH/381-449 gi|9106065|gb|AAF83920.1|AE003946_11_370:427 blasting: RECJ_ERWCH/381-449 gi|9656991|gb|AAF95560.1|_385:452 blasting: starting RECJ_HAEIN/376-445 with E=0.000050 RECJ_HAEIN/376-445 RECJ_HAEIN/376-445 blasting: RECJ_HAEIN/376-445 gi|96357|pir||C39202_383:452 blasting: RECJ_HAEIN/376-445 gi|2507106|sp|P21893|RECJ_ECOLI_382:451 blasting: RECJ_HAEIN/376-445 gi|1172895|sp|P45112|RECJ_HAEIN_376:445 blasting: RECJ_HAEIN/376-445 gi|2507107|sp|P39693|RECJ_ERWCH_381:447 blasting: RECJ_HAEIN/376-445 gi|7226077|gb|AAF41253.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|7228156|emb|CAB77039.1|_381:450 blasting: RECJ_HAEIN/376-445 gi|7379749|emb|CAB84317.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|7453624|gb|AAF62912.1|_377:446 blasting: RECJ_HAEIN/376-445 gi|9106065|gb|AAF83920.1|AE003946_11_370:439 blasting: RECJ_HAEIN/376-445 gi|9656991|gb|AAF95560.1|_385:454 blasting: starting P73518/390-455 with E=0.000050 P73518/390-455 P73518/390-455 blasting: P73518/390-455 gi|7470865|pir||S77224_391:454 blasting: starting O32044/370-436 with E=0.000050 O32044/370-436 O32044/370-436 blasting: O32044/370-436 gi|7475820|pir||H69980_371:436 blasting: starting O83702/514-575 with E=0.000050 O83702/514-575 O83702/514-575 blasting: O83702/514-575 gi|7521421|pir||D71289_515:575 blasting: starting Q9Z7Z0/390-454 with E=0.000050 Q9Z7Z0/390-454 Q9Z7Z0/390-454 blasting: Q9Z7Z0/390-454 gi|2126389|pir||PC4257_67:129 blasting: Q9Z7Z0/390-454 gi|3063673|gb|AAC14136.1|_318:380 blasting: Q9Z7Z0/390-454 gi|7451688|pir||H71513_390:452 blasting: Q9Z7Z0/390-454 gi|7451687|pir||D72062_391:453 blasting: Q9Z7Z0/390-454 gi|7190761|gb|AAF39542.1|_390:452 blasting: starting P94659/317-381 with E=0.000050 P94659/317-381 P94659/317-381 blasting: P94659/317-381 gi|2126389|pir||PC4257_68:129 blasting: P94659/317-381 gi|3063673|gb|AAC14136.1|_319:380 blasting: P94659/317-381 gi|7451688|pir||H71513_391:452 blasting: P94659/317-381 gi|7451687|pir||D72062_392:453 blasting: P94659/317-381 gi|7190761|gb|AAF39542.1|_391:452 blasting: starting O84453/389-453 with E=0.000050 O84453/389-453 O84453/389-453 blasting: O84453/389-453 gi|2126389|pir||PC4257_67:129 blasting: O84453/389-453 gi|3063673|gb|AAC14136.1|_318:380 blasting: O84453/389-453 gi|7451688|pir||H71513_390:452 blasting: O84453/389-453 gi|7451687|pir||D72062_391:453 blasting: O84453/389-453 gi|7190761|gb|AAF39542.1|_390:452 blasting: starting Q9ZD22/386-452 with E=0.000050 Q9ZD22/386-452 Q9ZD22/386-452 blasting: Q9ZD22/386-452 gi|7451686|pir||G71656_386:452 blasting: starting Q9ZMA0/338-403 with E=0.000050 Q9ZMA0/338-403 Q9ZMA0/338-403 blasting: Q9ZMA0/338-403 gi|7451683|pir||D64563_338:403 blasting: Q9ZMA0/338-403 gi|7451682|pir||B71946_338:403 blasting: starting O67909/370-434 with E=0.000050 O67909/370-434 O67909/370-434 blasting: O67909/370-434 gi|7451685|pir||A70485_370:434 blasting: starting Y371_MYCGE/252-315 with E=0.000050 Y371_MYCGE/252-315 Y371_MYCGE/252-315 blasting: Y371_MYCGE/252-315 gi|2496409|sp|Q49428|Y371_MYCGE_252:315 blasting: Y371_MYCGE/252-315 gi|2496410|sp|P75229|Y371_MYCPN_252:315 blasting: starting O51269/507-572 with E=0.000050 O51269/507-572 O51269/507-572 blasting: O51269/507-572 gi|7463775|pir||F70131_510:572 blasting: starting Q9ZM41/283-342 with E=0.000050 Q9ZM41/283-342 Q9ZM41/283-342 blasting: Q9ZM41/283-342 gi|7464457|pir||B64650_287:327 blasting: Q9ZM41/283-342 gi|7464457|pir||B64650_328:343 blasting: Q9ZM41/283-342 gi|7464707|pir||D71937_286:326 blasting: Q9ZM41/283-342 gi|7464707|pir||D71937_327:342 blasting: starting O67552/249-312 with E=0.000050 O67552/249-312 O67552/249-312 blasting: O67552/249-312 gi|7445472|pir||F70440_249:312 blasting: starting O51564/262-322 with E=0.000050 O51564/262-322 O51564/262-322 blasting: O51564/262-322 gi|7430137|pir||B70177_264:322 blasting: starting O83450/285-343 with E=0.000050 O83450/285-343 O83450/285-343 blasting: O83450/285-343 gi|7514584|pir||D71323_286:341 blasting: starting P71615/275-333 with E=0.000050 P71615/275-333 P71615/275-333 blasting: P71615/275-333 gi|7477397|pir||H70693_278:328 blasting: starting MGPA_MYCPN/261-317 with E=0.000050 MGPA_MYCPN/261-317 MGPA_MYCPN/261-317 blasting: MGPA_MYCPN/261-317 gi|80890|pir||JQ0091_190:239 blasting: MGPA_MYCPN/261-317 gi|80899|pir||JS0068_179:228 blasting: MGPA_MYCPN/261-317 gi|80899|pir||JS0068_200:234 blasting: MGPA_MYCPN/261-317 gi|1346531|sp|P22746|MGPA_MYCGE_298:347 blasting: MGPA_MYCPN/261-317 gi|2498554|sp|P75144|MGPA_MYCPN_262:311 blasting: MGPA_MYCPN/261-317 gi|2498554|sp|P75144|MGPA_MYCPN_283:317 blasting: starting MGPA_MYCGE/296-360 with E=0.000050 MGPA_MYCGE/296-360 MGPA_MYCGE/296-360 blasting: MGPA_MYCGE/296-360 gi|80890|pir||JQ0091_190:252 blasting: MGPA_MYCGE/296-360 gi|80899|pir||JS0068_179:239 blasting: MGPA_MYCGE/296-360 gi|1346531|sp|P22746|MGPA_MYCGE_298:360 blasting: MGPA_MYCGE/296-360 gi|2498554|sp|P75144|MGPA_MYCPN_262:322 blasting: starting O31824/247-305 with E=0.000050 O31824/247-305 O31824/247-305 blasting: O31824/247-305 gi|7475203|pir||A69893_259:305 blasting: O31824/247-305 gi|7475203|pir||A69893_247:258 blasting: starting YG33_METJA/394-461 with E=0.000050 YG33_METJA/394-461 YG33_METJA/394-461 blasting: YG33_METJA/394-461 gi|3025197|sp|Q59027|YG33_METJA_397:442 blasting: YG33_METJA/394-461 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: YG33_METJA/394-461 gi|7448978|pir||D69503_392:439 blasting: YG33_METJA/394-461 gi|7448978|pir||D69503_440:458 blasting: YG33_METJA/394-461 gi|7448980|pir||H71452_406:453 blasting: YG33_METJA/394-461 gi|7448980|pir||H71452_454:472 blasting: YG33_METJA/394-461 gi|7448979|pir||B75216_406:453 blasting: YG33_METJA/394-461 gi|7448979|pir||B75216_454:472 blasting: starting O58017/401-472 with E=0.000050 O58017/401-472 O58017/401-472 blasting: O58017/401-472 gi|3025197|sp|Q59027|YG33_METJA_396:442 blasting: O58017/401-472 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: O58017/401-472 gi|7448978|pir||D69503_389:439 blasting: O58017/401-472 gi|7448978|pir||D69503_440:458 blasting: O58017/401-472 gi|7448980|pir||H71452_403:453 blasting: O58017/401-472 gi|7448980|pir||H71452_454:472 blasting: O58017/401-472 gi|7448979|pir||B75216_403:453 blasting: O58017/401-472 gi|7448979|pir||B75216_454:472 blasting: starting O28250/387-458 with E=0.000050 O28250/387-458 O28250/387-458 blasting: O28250/387-458 gi|3025197|sp|Q59027|YG33_METJA_396:442 blasting: O28250/387-458 gi|3025197|sp|Q59027|YG33_METJA_443:461 blasting: O28250/387-458 gi|7448978|pir||D69503_389:439 blasting: O28250/387-458 gi|7448978|pir||D69503_440:458 blasting: O28250/387-458 gi|7448980|pir||H71452_403:453 blasting: O28250/387-458 gi|7448980|pir||H71452_454:472 blasting: O28250/387-458 gi|7448979|pir||B75216_403:453 blasting: O28250/387-458 gi|7448979|pir||B75216_454:472 blasting: starting Y988_METJA/239-310 with E=0.000050 Y988_METJA/239-310 Y988_METJA/239-310 blasting: Y988_METJA/239-310 gi|3024962|sp|Q58395|Y988_METJA_241:297 blasting: Y988_METJA/239-310 gi|3024962|sp|Q58395|Y988_METJA_298:310 blasting: Y988_METJA/239-310 gi|7518694|pir||B71167_251:303 blasting: Y988_METJA/239-310 gi|7518105|pir||C75065_252:304 blasting: starting O73979/249-318 with E=0.000050 O73979/249-318 O73979/249-318 blasting: O73979/249-318 gi|3024962|sp|Q58395|Y988_METJA_246:295 blasting: O73979/249-318 gi|7450700|pir||B69086_377:425 blasting: O73979/249-318 gi|7450705|pir||G69341_383:433 blasting: O73979/249-318 gi|7518694|pir||B71167_252:318 blasting: O73979/249-318 gi|7518105|pir||C75065_253:319 blasting: starting Y977_METJA/396-466 with E=0.000050 Y977_METJA/396-466 Y977_METJA/396-466 blasting: Y977_METJA/396-466 gi|2842584|sp|Q58387|RECJ_METJA_399:466 blasting: Y977_METJA/396-466 gi|7450700|pir||B69086_374:437 blasting: Y977_METJA/396-466 gi|7450705|pir||G69341_382:445 blasting: Y977_METJA/396-466 gi|7450702|pir||C69337_371:427 blasting: starting O26266/371-441 with E=0.000050 O26266/371-441 O26266/371-441 blasting: O26266/371-441 gi|2842584|sp|Q58387|RECJ_METJA_404:465 blasting: O26266/371-441 gi|7450700|pir||B69086_371:440 blasting: O26266/371-441 gi|7450705|pir||G69341_387:448 blasting: O26266/371-441 gi|7450702|pir||C69337_376:430 blasting: O26266/371-441 gi|7450704|pir||H71224_408:464 blasting: O26266/371-441 gi|7518694|pir||B71167_259:302 blasting: O26266/371-441 gi|7450703|pir||G75192_409:465 blasting: O26266/371-441 gi|7518105|pir||C75065_260:303 blasting: starting O57804/392-465 with E=0.000050 O57804/392-465 O57804/392-465 blasting: O57804/392-465 gi|7450700|pir||B69086_372:440 blasting: O57804/392-465 gi|7450701|pir||E69056_392:448 blasting: O57804/392-465 gi|7450705|pir||G69341_380:448 blasting: O57804/392-465 gi|7450702|pir||C69337_363:430 blasting: O57804/392-465 gi|7450704|pir||H71224_393:464 blasting: O57804/392-465 gi|7450703|pir||G75192_394:465 blasting: starting O29523/379-449 with E=0.000050 O29523/379-449 O29523/379-449 blasting: O29523/379-449 gi|2833617|sp|Q58241|Y831_METJA_355:423 blasting: O29523/379-449 gi|2842584|sp|Q58387|RECJ_METJA_397:465 blasting: O29523/379-449 gi|7450700|pir||B69086_372:440 blasting: O29523/379-449 gi|7450701|pir||E69056_389:448 blasting: O29523/379-449 gi|7450705|pir||G69341_379:448 blasting: O29523/379-449 gi|7450702|pir||C69337_362:430 blasting: O29523/379-449 gi|7450704|pir||H71224_392:464 blasting: O29523/379-449 gi|7518694|pir||B71167_256:315 blasting: O29523/379-449 gi|7450703|pir||G75192_393:465 blasting: O29523/379-449 gi|7518105|pir||C75065_257:316 blasting: starting O27473/379-449 with E=0.000050 O27473/379-449 O27473/379-449 blasting: O27473/379-449 gi|2833617|sp|Q58241|Y831_METJA_369:424 blasting: O27473/379-449 gi|7450700|pir||B69086_374:440 blasting: O27473/379-449 gi|7450701|pir||E69056_382:449 blasting: O27473/379-449 gi|7450705|pir||G69341_382:448 blasting: O27473/379-449 gi|7450702|pir||C69337_365:430 blasting: O27473/379-449 gi|7450704|pir||H71224_408:465 blasting: O27473/379-449 gi|7450703|pir||G75192_409:466 blasting: starting O29559/362-431 with E=0.000050 O29559/362-431 O29559/362-431 blasting: O29559/362-431 gi|2833617|sp|Q58241|Y831_METJA_355:423 blasting: O29559/362-431 gi|2842584|sp|Q58387|RECJ_METJA_406:465 blasting: O29559/362-431 gi|7450705|pir||G69341_379:448 blasting: O29559/362-431 gi|7450702|pir||C69337_362:430 blasting: starting Y831_METJA/355-424 with E=0.000050 Y831_METJA/355-424 Y831_METJA/355-424 blasting: Y831_METJA/355-424 gi|2833617|sp|Q58241|Y831_METJA_355:424 blasting: Y831_METJA/355-424 gi|7450701|pir||E69056_393:449 blasting: Y831_METJA/355-424 gi|7450705|pir||G69341_379:448 blasting: Y831_METJA/355-424 gi|7450702|pir||C69337_362:430 blasting: starting YYBT_BACSU/588-647 with E=0.000050 YYBT_BACSU/588-647 YYBT_BACSU/588-647 blasting: YYBT_BACSU/588-647 gi|586814|sp|P37484|YYBT_BACSU_588:646 blasting: starting O66728/230-290 with E=0.000050 O66728/230-290 O66728/230-290 blasting: O66728/230-290 gi|7520820|pir||D70337_233:284 blasting: starting O58035/847-912 with E=0.000050 O58035/847-912 O58035/847-912 blasting: O58035/847-912 gi|6707751|sp|O58035|SYA_PYRHO_849:912 blasting: O58035/847-912 gi|7437620|pir||B75017_849:908 blasting: starting SYA_ARCFU/831-899 with E=0.000050 SYA_ARCFU/831-899 SYA_ARCFU/831-899 blasting: SYA_ARCFU/831-899 gi|3334348|sp|O28029|SYA_ARCFU_831:898 blasting: starting O67323/793-863 with E=0.000050 O67323/793-863 O67323/793-863 blasting: O67323/793-863 gi|145220|gb|AAA03208.1|_801:868 blasting: O67323/793-863 gi|1174496|sp|P43815|SYA_HAEIN_800:868 blasting: O67323/793-863 gi|2500957|sp|P70865|SYA_BARBA_813:882 blasting: O67323/793-863 gi|2507425|sp|P00957|SYA_ECOLI_801:868 blasting: O67323/793-863 gi|2281029|dbj|BAA21554.1|_3:70 blasting: O67323/793-863 gi|3122886|sp|O34526|SYA_BACSU_803:872 blasting: O67323/793-863 gi|6226165|sp|O67323|SYA_AQUAE_795:863 blasting: O67323/793-863 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:863 blasting: O67323/793-863 gi|6707752|sp|Q9X1B6|SYA_THEMA_792:860 blasting: O67323/793-863 gi|7226845|gb|AAF41948.1|_799:867 blasting: starting SYA_THIFE/800-870 with E=0.000050 SYA_THIFE/800-870 SYA_THIFE/800-870 blasting: SYA_THIFE/800-870 gi|145220|gb|AAA03208.1|_802:864 blasting: SYA_THIFE/800-870 gi|1174496|sp|P43815|SYA_HAEIN_801:852 blasting: SYA_THIFE/800-870 gi|2500961|sp|Q56273|SYA_THIFE_803:870 blasting: SYA_THIFE/800-870 gi|2507425|sp|P00957|SYA_ECOLI_802:864 blasting: SYA_THIFE/800-870 gi|2281029|dbj|BAA21554.1|_4:66 blasting: SYA_THIFE/800-870 gi|3122886|sp|O34526|SYA_BACSU_804:867 blasting: SYA_THIFE/800-870 gi|3293580|gb|AAC25784.1|_1:54 blasting: SYA_THIFE/800-870 gi|7226845|gb|AAF41948.1|_800:864 blasting: SYA_THIFE/800-870 gi|7380429|emb|CAB85015.1|_800:862 blasting: SYA_THIFE/800-870 gi|9104908|gb|AAF82937.1|AE003866_2_841:905 blasting: SYA_THIFE/800-870 gi|9654973|gb|AAF93713.1|_787:851 blasting: starting SYA_ECOLI/799-869 with E=0.000050 SYA_ECOLI/799-869 SYA_ECOLI/799-869 blasting: SYA_ECOLI/799-869 gi|145220|gb|AAA03208.1|_801:869 blasting: SYA_ECOLI/799-869 gi|1174496|sp|P43815|SYA_HAEIN_800:854 blasting: SYA_ECOLI/799-869 gi|2500961|sp|Q56273|SYA_THIFE_802:864 blasting: SYA_ECOLI/799-869 gi|2500957|sp|P70865|SYA_BARBA_812:869 blasting: SYA_ECOLI/799-869 gi|2500959|sp|P74423|SYA_SYNY3_800:864 blasting: SYA_ECOLI/799-869 gi|2507425|sp|P00957|SYA_ECOLI_801:869 blasting: SYA_ECOLI/799-869 gi|2281029|dbj|BAA21554.1|_3:71 blasting: SYA_ECOLI/799-869 gi|3122886|sp|O34526|SYA_BACSU_803:866 blasting: SYA_ECOLI/799-869 gi|6226165|sp|O67323|SYA_AQUAE_795:857 blasting: SYA_ECOLI/799-869 gi|3293580|gb|AAC25784.1|_1:51 blasting: SYA_ECOLI/799-869 gi|5834358|gb|AAD53924.1|AF179611_8_814:868 blasting: SYA_ECOLI/799-869 gi|7471091|pir||F75289_828:885 blasting: SYA_ECOLI/799-869 gi|6967975|emb|CAB75143.1|_771:830 blasting: SYA_ECOLI/799-869 gi|7226845|gb|AAF41948.1|_799:860 blasting: SYA_ECOLI/799-869 gi|7380429|emb|CAB85015.1|_799:859 blasting: SYA_ECOLI/799-869 gi|7404473|sp|P27866|SYA_RHIME_822:870 blasting: SYA_ECOLI/799-869 gi|8249960|emb|CAB93381.1|_814:874 blasting: SYA_ECOLI/799-869 gi|9104908|gb|AAF82937.1|AE003866_2_840:903 blasting: SYA_ECOLI/799-869 gi|9654973|gb|AAF93713.1|_786:848 blasting: starting SYA_BACSU/801-872 with E=0.000050 SYA_BACSU/801-872 SYA_BACSU/801-872 blasting: SYA_BACSU/801-872 gi|135089|sp|P21894|SYA_BOMMO_900:955 blasting: SYA_BACSU/801-872 gi|145220|gb|AAA03208.1|_801:864 blasting: SYA_BACSU/801-872 gi|1174496|sp|P43815|SYA_HAEIN_800:863 blasting: SYA_BACSU/801-872 gi|2500961|sp|Q56273|SYA_THIFE_802:865 blasting: SYA_BACSU/801-872 gi|2500957|sp|P70865|SYA_BARBA_812:877 blasting: SYA_BACSU/801-872 gi|2500959|sp|P74423|SYA_SYNY3_800:865 blasting: SYA_BACSU/801-872 gi|2507425|sp|P00957|SYA_ECOLI_801:864 blasting: SYA_BACSU/801-872 gi|2281029|dbj|BAA21554.1|_3:66 blasting: SYA_BACSU/801-872 gi|3334347|sp|O27718|SYA_METTH_830:886 blasting: SYA_BACSU/801-872 gi|3122886|sp|O34526|SYA_BACSU_803:872 blasting: SYA_BACSU/801-872 gi|7450705|pir||G69341_382:441 blasting: SYA_BACSU/801-872 gi|6226165|sp|O67323|SYA_AQUAE_795:858 blasting: SYA_BACSU/801-872 gi|7518694|pir||B71167_251:312 blasting: SYA_BACSU/801-872 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_BACSU/801-872 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:858 blasting: SYA_BACSU/801-872 gi|6707752|sp|Q9X1B6|SYA_THEMA_792:855 blasting: SYA_BACSU/801-872 gi|7518105|pir||C75065_252:313 blasting: SYA_BACSU/801-872 gi|5834358|gb|AAD53924.1|AF179611_8_814:878 blasting: SYA_BACSU/801-872 gi|7471091|pir||F75289_826:875 blasting: SYA_BACSU/801-872 gi|6967975|emb|CAB75143.1|_771:831 blasting: SYA_BACSU/801-872 gi|7226845|gb|AAF41948.1|_799:862 blasting: SYA_BACSU/801-872 gi|7380429|emb|CAB85015.1|_799:862 blasting: SYA_BACSU/801-872 gi|7404473|sp|P27866|SYA_RHIME_814:878 blasting: SYA_BACSU/801-872 gi|8249960|emb|CAB93381.1|_814:878 blasting: SYA_BACSU/801-872 gi|9654973|gb|AAF93713.1|_786:849 blasting: starting SYA_HAEIN/798-868 with E=0.000050 SYA_HAEIN/798-868 SYA_HAEIN/798-868 blasting: SYA_HAEIN/798-868 gi|145220|gb|AAA03208.1|_802:864 blasting: SYA_HAEIN/798-868 gi|1174496|sp|P43815|SYA_HAEIN_801:866 blasting: SYA_HAEIN/798-868 gi|2500961|sp|Q56273|SYA_THIFE_803:868 blasting: SYA_HAEIN/798-868 gi|2500957|sp|P70865|SYA_BARBA_813:877 blasting: SYA_HAEIN/798-868 gi|2507425|sp|P00957|SYA_ECOLI_802:864 blasting: SYA_HAEIN/798-868 gi|2281029|dbj|BAA21554.1|_4:66 blasting: SYA_HAEIN/798-868 gi|3024653|sp|P56452|SYA_HELPY_782:837 blasting: SYA_HAEIN/798-868 gi|3122886|sp|O34526|SYA_BACSU_804:867 blasting: SYA_HAEIN/798-868 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_HAEIN/798-868 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_782:837 blasting: SYA_HAEIN/798-868 gi|5834358|gb|AAD53924.1|AF179611_8_815:879 blasting: SYA_HAEIN/798-868 gi|6967975|emb|CAB75143.1|_772:832 blasting: SYA_HAEIN/798-868 gi|7226845|gb|AAF41948.1|_800:858 blasting: SYA_HAEIN/798-868 gi|7380429|emb|CAB85015.1|_800:853 blasting: SYA_HAEIN/798-868 gi|7404473|sp|P27866|SYA_RHIME_814:879 blasting: SYA_HAEIN/798-868 gi|9654973|gb|AAF93713.1|_787:850 blasting: starting SYA_BARBA/810-882 with E=0.000050 SYA_BARBA/810-882 SYA_BARBA/810-882 blasting: SYA_BARBA/810-882 gi|145220|gb|AAA03208.1|_801:866 blasting: SYA_BARBA/810-882 gi|1174496|sp|P43815|SYA_HAEIN_800:863 blasting: SYA_BARBA/810-882 gi|2500957|sp|P70865|SYA_BARBA_812:882 blasting: SYA_BARBA/810-882 gi|2507425|sp|P00957|SYA_ECOLI_801:866 blasting: SYA_BARBA/810-882 gi|2281029|dbj|BAA21554.1|_3:68 blasting: SYA_BARBA/810-882 gi|6226165|sp|O67323|SYA_AQUAE_795:858 blasting: SYA_BARBA/810-882 gi|5834358|gb|AAD53924.1|AF179611_8_814:880 blasting: SYA_BARBA/810-882 gi|7380429|emb|CAB85015.1|_799:864 blasting: SYA_BARBA/810-882 gi|7404473|sp|P27866|SYA_RHIME_813:880 blasting: SYA_BARBA/810-882 gi|9654973|gb|AAF93713.1|_786:849 blasting: starting SYA_SYNY3/797-870 with E=0.000050 SYA_SYNY3/797-870 SYA_SYNY3/797-870 blasting: SYA_SYNY3/797-870 gi|145220|gb|AAA03208.1|_802:866 blasting: SYA_SYNY3/797-870 gi|1174496|sp|P43815|SYA_HAEIN_801:866 blasting: SYA_SYNY3/797-870 gi|2500961|sp|Q56273|SYA_THIFE_803:868 blasting: SYA_SYNY3/797-870 gi|2500959|sp|P74423|SYA_SYNY3_799:868 blasting: SYA_SYNY3/797-870 gi|2507425|sp|P00957|SYA_ECOLI_802:866 blasting: SYA_SYNY3/797-870 gi|2281029|dbj|BAA21554.1|_4:68 blasting: SYA_SYNY3/797-870 gi|3334347|sp|O27718|SYA_METTH_825:889 blasting: SYA_SYNY3/797-870 gi|3122886|sp|O34526|SYA_BACSU_802:869 blasting: SYA_SYNY3/797-870 gi|3293580|gb|AAC25784.1|_1:52 blasting: SYA_SYNY3/797-870 gi|6707748|sp|Q9XDM3|SYA_AQUPY_795:858 blasting: SYA_SYNY3/797-870 gi|6967975|emb|CAB75143.1|_770:831 blasting: SYA_SYNY3/797-870 gi|7226845|gb|AAF41948.1|_798:862 blasting: SYA_SYNY3/797-870 gi|7380429|emb|CAB85015.1|_798:864 blasting: SYA_SYNY3/797-870 gi|8249960|emb|CAB93381.1|_813:878 blasting: SYA_SYNY3/797-870 gi|9654973|gb|AAF93713.1|_787:849 blasting: starting Q9ZCA4/802-873 with E=0.000050 Q9ZCA4/802-873 Q9ZCA4/802-873 blasting: Q9ZCA4/802-873 gi|6226166|sp|Q9ZCA4|SYA_RICPR_803:872 blasting: starting SYA_METJA/829-887 with E=0.000050 SYA_METJA/829-887 SYA_METJA/829-887 blasting: SYA_METJA/829-887 gi|2500963|sp|Q57984|SYA_METJA_831:887 blasting: starting Q9Z714/793-865 with E=0.000050 Q9Z714/793-865 Q9Z714/793-865 blasting: Q9Z714/793-865 gi|6707750|sp|Q9Z714|SYA_CHLPN_795:865 blasting: Q9Z714/793-865 gi|6707747|sp|O84754|SYA_CHLTR_799:868 blasting: Q9Z714/793-865 gi|7190160|gb|AAF39003.1|_799:868 blasting: Q9Z714/793-865 gi|7437632|pir||E71476_848:917 blasting: starting O84754/846-917 with E=0.000050 O84754/846-917 O84754/846-917 blasting: O84754/846-917 gi|6707750|sp|Q9Z714|SYA_CHLPN_796:863 blasting: O84754/846-917 gi|6707747|sp|O84754|SYA_CHLTR_799:867 blasting: O84754/846-917 gi|7190160|gb|AAF39003.1|_799:867 blasting: O84754/846-917 gi|7437632|pir||E71476_848:916 blasting: starting O57734/333-400 with E=0.000050 O57734/333-400 O57734/333-400 blasting: O57734/333-400 gi|7514241|pir||A71213_340:400 blasting: O57734/333-400 gi|7514241|pir||A71213_333:339 blasting: O57734/333-400 gi|7514245|pir||G75027_341:400 blasting: starting SYAC_SCHPO/881-951 with E=0.000050 SYAC_SCHPO/881-951 SYAC_SCHPO/881-951 blasting: SYAC_SCHPO/881-951 gi|609338|gb|AAC49007.1|_877:947 blasting: SYAC_SCHPO/881-951 gi|3183171|sp|O13914|SYAC_SCHPO_881:951 blasting: starting SYAC_YEAST/877-950 with E=0.000050 SYAC_YEAST/877-950 SYAC_YEAST/877-950 blasting: SYAC_YEAST/877-950 gi|609338|gb|AAC49007.1|_877:947 blasting: SYAC_YEAST/877-950 gi|3183171|sp|O13914|SYAC_SCHPO_881:948 blasting: starting SYA_METTH/817-891 with E=0.000050 SYA_METTH/817-891 SYA_METTH/817-891 blasting: SYA_METTH/817-891 gi|2500959|sp|P74423|SYA_SYNY3_799:865 blasting: SYA_METTH/817-891 gi|3334347|sp|O27718|SYA_METTH_817:888 blasting: SYA_METTH/817-891 gi|3122886|sp|O34526|SYA_BACSU_811:867 blasting: SYA_METTH/817-891 gi|6226165|sp|O67323|SYA_AQUAE_794:859 blasting: SYA_METTH/817-891 gi|6707748|sp|Q9XDM3|SYA_AQUPY_794:859 blasting: SYA_METTH/817-891 gi|6176442|gb|AAF05593.1|AF188718_1_904:955 blasting: SYA_METTH/817-891 gi|7297398|gb|AAF52657.1|_904:955 blasting: starting SYA_THETH/808-882 with E=0.000050 SYA_THETH/808-882 SYA_THETH/808-882 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_830:882 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_808:829 blasting: SYA_THETH/808-882 gi|2500960|sp|P74941|SYA_THETH_478:492 blasting: starting SYA_MYCTU/821-895 with E=0.000050 SYA_MYCTU/821-895 SYA_MYCTU/821-895 blasting: SYA_MYCTU/821-895 gi|3122879|sp|O07438|SYA_MYCTU_821:895 blasting: SYA_MYCTU/821-895 gi|8249960|emb|CAB93381.1|_813:879 blasting: starting O01541/890-961 with E=0.000050 O01541/890-961 O01541/890-961 blasting: O01541/890-961 gi|135089|sp|P21894|SYA_BOMMO_891:958 blasting: O01541/890-961 gi|7500106|pir||T29466_891:959 blasting: O01541/890-961 gi|3024653|sp|P56452|SYA_HELPY_791:837 blasting: O01541/890-961 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_796:837 blasting: O01541/890-961 gi|6176440|gb|AAF05592.1|AF188717_1_870:936 blasting: O01541/890-961 gi|6176442|gb|AAF05593.1|AF188718_1_890:957 blasting: O01541/890-961 gi|7297398|gb|AAF52657.1|_890:957 blasting: starting SYA_HUMAN/886-957 with E=0.000050 SYA_HUMAN/886-957 SYA_HUMAN/886-957 blasting: SYA_HUMAN/886-957 gi|135089|sp|P21894|SYA_BOMMO_890:957 blasting: SYA_HUMAN/886-957 gi|7500106|pir||T29466_892:958 blasting: SYA_HUMAN/886-957 gi|3024653|sp|P56452|SYA_HELPY_775:836 blasting: SYA_HUMAN/886-957 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_775:836 blasting: SYA_HUMAN/886-957 gi|6176440|gb|AAF05592.1|AF188717_1_871:936 blasting: SYA_HUMAN/886-957 gi|6176442|gb|AAF05593.1|AF188718_1_889:956 blasting: SYA_HUMAN/886-957 gi|7297398|gb|AAF52657.1|_889:956 blasting: starting SYA_BOMMO/889-960 with E=0.000050 SYA_BOMMO/889-960 SYA_BOMMO/889-960 blasting: SYA_BOMMO/889-960 gi|135089|sp|P21894|SYA_BOMMO_890:960 blasting: SYA_BOMMO/889-960 gi|7500106|pir||T29466_892:961 blasting: SYA_BOMMO/889-960 gi|3122886|sp|O34526|SYA_BACSU_812:867 blasting: SYA_BOMMO/889-960 gi|6176440|gb|AAF05592.1|AF188717_1_871:941 blasting: SYA_BOMMO/889-960 gi|6176442|gb|AAF05593.1|AF188718_1_889:959 blasting: SYA_BOMMO/889-960 gi|7297398|gb|AAF52657.1|_889:959 blasting: starting SYA_HELPY/772-839 with E=0.000050 SYA_HELPY/772-839 SYA_HELPY/772-839 blasting: SYA_HELPY/772-839 gi|3024653|sp|P56452|SYA_HELPY_775:839 blasting: SYA_HELPY/772-839 gi|3293580|gb|AAC25784.1|_14:53 blasting: SYA_HELPY/772-839 gi|6707753|sp|Q9ZJY5|SYA_HELPJ_775:839 blasting: SYA_HELPY/772-839 gi|6967975|emb|CAB75143.1|_773:831 blasting: starting SYA_ARATH/923-996 with E=0.000050 SYA_ARATH/923-996 SYA_ARATH/923-996 blasting: SYA_ARATH/923-996 gi|421855|pir||S32671_910:979 blasting: SYA_ARATH/923-996 gi|2507426|sp|P36428|SYA_ARATH_924:993 blasting: SYA_ARATH/923-996 gi|1673366|emb|CAA80381.1|_876:945 blasting: SYA_ARATH/923-996 gi|2065021|emb|CAA73145.1|_172:241 blasting: SYA_ARATH/923-996 gi|5734779|gb|AAD50044.1|AC007980_9_876:945 blasting: make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' make -k pf02272-tuned.t2k.a2m.gz \ pf02272-tuned.t2k.pa \ pf02272-tuned.t2k.pa.html \ pf02272-tuned.t2k.2d \ pf02272-tuned.t2k.tree \ pf02272-tuned.t2k_sorted.pa \ pf02272-tuned.t2k.tree.ps \ pf02272-tuned.t2k.tree-unroot.ps make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' /projects/compbio/experiments/models.97/scripts2k/target2k -out pf02272-tuned.t2k \ -seed pf02272-tuned.seq \ -all @@@@ chgrp protein /projects/compbio/tmp/target2k-beta-21999 @@@@ cp /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.seq m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52 # About to count sequences in /projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are prefilter: 0.01, actual: 0.0001 prefilter: 1, actual: 0.0002 prefilter: 10, actual: 0.001 prefilter: 400, actual: 0.005 /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.6, 0.5 /projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 541007 reverse_diff= 4 /projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 20000 /projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10 /projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1 /projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1 @@@@ blast-prefilter -out prefilter -seed m0.a2m -prefilter_thresholds 0.01,1,10,400 -db /projects/compbio/data/nrp/nr -blast_max_report 20000 @@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-25257 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /export/projects/compbio/tmp/target2k-beta-21999/prefilter_1.fa, 0.01 For /export/projects/compbio/tmp/target2k-beta-21999/prefilter_2.fa, 1 For /export/projects/compbio/tmp/target2k-beta-21999/prefilter_3.fa, 10 For /export/projects/compbio/tmp/target2k-beta-21999/prefilter_4.fa, 400 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-21999/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /export/projects/compbio/tmp/target2k-beta-21999/m0.a2m (120 sequences, 74 columns) as A2M alignment. Writing sequence output to init.a2m. Dropping 0 (of 120) duplicate sequences with identical IDs 60 sequences left after dropping 60 of 120 sequences. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=400 V=20000 B=0 -gi > 1.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 1.fasta < /dev/null @@@@ rm -f 1.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 2.fasta E=400 V=20000 B=0 -gi > 2.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 2.fasta < /dev/null @@@@ rm -f 2.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 3.fasta E=400 V=20000 B=0 -gi > 3.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 3.fasta < /dev/null @@@@ rm -f 3.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 4.fasta E=400 V=20000 B=0 -gi > 4.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 4.fasta < /dev/null @@@@ rm -f 4.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 5.fasta E=400 V=20000 B=0 -gi > 5.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 5.fasta < /dev/null @@@@ rm -f 5.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 6.fasta E=400 V=20000 B=0 -gi > 6.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 6.fasta < /dev/null @@@@ rm -f 6.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 7.fasta E=400 V=20000 B=0 -gi > 7.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 7.fasta < /dev/null @@@@ rm -f 7.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 8.fasta E=400 V=20000 B=0 -gi > 8.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 8.fasta < /dev/null @@@@ rm -f 8.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 9.fasta E=400 V=20000 B=0 -gi > 9.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 9.fasta < /dev/null @@@@ rm -f 9.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 10.fasta E=400 V=20000 B=0 -gi > 10.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 10.fasta < /dev/null @@@@ rm -f 10.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 11.fasta E=400 V=20000 B=0 -gi > 11.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 11.fasta < /dev/null @@@@ rm -f 11.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 12.fasta E=400 V=20000 B=0 -gi > 12.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 12.fasta < /dev/null @@@@ rm -f 12.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 13.fasta E=400 V=20000 B=0 -gi > 13.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 13.fasta < /dev/null @@@@ rm -f 13.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 14.fasta E=400 V=20000 B=0 -gi > 14.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 14.fasta < /dev/null @@@@ rm -f 14.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 15.fasta E=400 V=20000 B=0 -gi > 15.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 15.fasta < /dev/null @@@@ rm -f 15.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 16.fasta E=400 V=20000 B=0 -gi > 16.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 16.fasta < /dev/null @@@@ rm -f 16.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 17.fasta E=400 V=20000 B=0 -gi > 17.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 17.fasta < /dev/null @@@@ rm -f 17.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 18.fasta E=400 V=20000 B=0 -gi > 18.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 18.fasta < /dev/null @@@@ rm -f 18.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 19.fasta E=400 V=20000 B=0 -gi > 19.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 19.fasta < /dev/null @@@@ rm -f 19.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 20.fasta E=400 V=20000 B=0 -gi > 20.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 20.fasta < /dev/null @@@@ rm -f 20.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 21.fasta E=400 V=20000 B=0 -gi > 21.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 21.fasta < /dev/null @@@@ rm -f 21.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 22.fasta E=400 V=20000 B=0 -gi > 22.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 22.fasta < /dev/null @@@@ rm -f 22.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 23.fasta E=400 V=20000 B=0 -gi > 23.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 23.fasta < /dev/null @@@@ rm -f 23.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 24.fasta E=400 V=20000 B=0 -gi > 24.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 24.fasta < /dev/null @@@@ rm -f 24.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 25.fasta E=400 V=20000 B=0 -gi > 25.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 25.fasta < /dev/null @@@@ rm -f 25.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 26.fasta E=400 V=20000 B=0 -gi > 26.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 26.fasta < /dev/null @@@@ rm -f 26.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 27.fasta E=400 V=20000 B=0 -gi > 27.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 27.fasta < /dev/null @@@@ rm -f 27.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 28.fasta E=400 V=20000 B=0 -gi > 28.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 28.fasta < /dev/null @@@@ rm -f 28.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 29.fasta E=400 V=20000 B=0 -gi > 29.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 29.fasta < /dev/null @@@@ rm -f 29.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 30.fasta E=400 V=20000 B=0 -gi > 30.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 30.fasta < /dev/null @@@@ rm -f 30.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 31.fasta E=400 V=20000 B=0 -gi > 31.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 31.fasta < /dev/null @@@@ rm -f 31.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 32.fasta E=400 V=20000 B=0 -gi > 32.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 32.fasta < /dev/null @@@@ rm -f 32.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 33.fasta E=400 V=20000 B=0 -gi > 33.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 33.fasta < /dev/null @@@@ rm -f 33.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 34.fasta E=400 V=20000 B=0 -gi > 34.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 34.fasta < /dev/null @@@@ rm -f 34.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 35.fasta E=400 V=20000 B=0 -gi > 35.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 35.fasta < /dev/null @@@@ rm -f 35.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 36.fasta E=400 V=20000 B=0 -gi > 36.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 36.fasta < /dev/null @@@@ rm -f 36.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 37.fasta E=400 V=20000 B=0 -gi > 37.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 37.fasta < /dev/null @@@@ rm -f 37.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 38.fasta E=400 V=20000 B=0 -gi > 38.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 38.fasta < /dev/null @@@@ rm -f 38.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 39.fasta E=400 V=20000 B=0 -gi > 39.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 39.fasta < /dev/null @@@@ rm -f 39.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 40.fasta E=400 V=20000 B=0 -gi > 40.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 40.fasta < /dev/null @@@@ rm -f 40.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 41.fasta E=400 V=20000 B=0 -gi > 41.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 41.fasta < /dev/null @@@@ rm -f 41.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 42.fasta E=400 V=20000 B=0 -gi > 42.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 42.fasta < /dev/null @@@@ rm -f 42.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 43.fasta E=400 V=20000 B=0 -gi > 43.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 43.fasta < /dev/null @@@@ rm -f 43.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 44.fasta E=400 V=20000 B=0 -gi > 44.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 44.fasta < /dev/null @@@@ rm -f 44.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 45.fasta E=400 V=20000 B=0 -gi > 45.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 45.fasta < /dev/null @@@@ rm -f 45.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 46.fasta E=400 V=20000 B=0 -gi > 46.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 46.fasta < /dev/null @@@@ rm -f 46.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 47.fasta E=400 V=20000 B=0 -gi > 47.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 47.fasta < /dev/null @@@@ rm -f 47.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 48.fasta E=400 V=20000 B=0 -gi > 48.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 48.fasta < /dev/null @@@@ rm -f 48.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 49.fasta E=400 V=20000 B=0 -gi > 49.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 49.fasta < /dev/null @@@@ rm -f 49.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 50.fasta E=400 V=20000 B=0 -gi > 50.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 50.fasta < /dev/null @@@@ rm -f 50.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 51.fasta E=400 V=20000 B=0 -gi > 51.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 51.fasta < /dev/null @@@@ rm -f 51.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 52.fasta E=400 V=20000 B=0 -gi > 52.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 52.fasta < /dev/null @@@@ rm -f 52.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 53.fasta E=400 V=20000 B=0 -gi > 53.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 53.fasta < /dev/null @@@@ rm -f 53.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 54.fasta E=400 V=20000 B=0 -gi > 54.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 54.fasta < /dev/null @@@@ rm -f 54.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 55.fasta E=400 V=20000 B=0 -gi > 55.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 55.fasta < /dev/null @@@@ rm -f 55.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 56.fasta E=400 V=20000 B=0 -gi > 56.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 56.fasta < /dev/null @@@@ rm -f 56.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 57.fasta E=400 V=20000 B=0 -gi > 57.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 57.fasta < /dev/null @@@@ rm -f 57.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 58.fasta E=400 V=20000 B=0 -gi > 58.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 58.fasta < /dev/null @@@@ rm -f 58.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 59.fasta E=400 V=20000 B=0 -gi > 59.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 59.fasta < /dev/null @@@@ rm -f 59.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 60.fasta E=400 V=20000 B=0 -gi > 60.fasta-blast.out Searched 541007 sequences # parsing wu-blastp output @@@@ rm -f 60.fasta < /dev/null @@@@ rm -f 60.fasta-blast.out < /dev/null # Extracting hits in FASTA format from /projects/compbio/data/nrp/nr @@@@ rm -rf /projects/compbio/tmp/blast-prefilter-beta-25257 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file m0.a2m (120 sequences, 74 columns) as A2M alignment. # About to count sequences in m0.a2m # About to count sequences in prefilter_1.fa @@@@ modelfromalign tmp_1-a -alignfile m0.a2m \ -insert /projects/compbio/lib/gap1.5.regularizer \ -aweight_bits 0.8\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst Reading parameter file /projects/compbio/lib/gap1.5.regularizer /projects/compbio/lib/gap1.5.regularizer(1): Reading REGULARIZER: gap1.5. Weak regularizer, gaps average 1.5, matches average 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file m0.a2m (120 sequences, 74 columns) as A2M alignment. @@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -simple_threshold -26.4115278685381 -Emax 0.0001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.27027027027027 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(21): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -38.088696 Database has 17 sequences with 12660 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_1-a.mult (13 sequences, 74 columns) as A2M alignment. Reading scores from file tmp_1-a.mstat Writing sequence output to tmp_1-a-sort.a2m. @@@@ cat m0.a2m tmp_1-a-sort.a2m > tmp_1-a.train.seq @@@@ cat m0.cst tmp_1-a-md.cst > tmp_1-a.train.cst # About to count sequences in tmp_1-a.train.seq # num_seqs=133 nll_thresh=-22.4115278685381 frac_id=0.87486054175488 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.87486054175488 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_1-a.train.seq (133 sequences, 74 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 4 (of 133) duplicate sequences with differing IDs Dropping 4 (of 133) duplicate sequences with identical IDs Dropping 7 (of 133) sequences with > 87.5% id 62 sequences left after dropping 71 of 133 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_1-a.train.seq \ -aweight_bits 0.8\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_1-a.train.seq (62 sequences, 74 columns) as A2M alignment. @@@@ buildmodel tmp_1-b -insert tmp_1-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_1-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/gap1.5.regularizer -sequence_weights tmp_1-a.w -constraints tmp_1-a.train.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(21): Reading MODEL -- Model from alignment file m0.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/gap1.5.regularizer /projects/compbio/lib/gap1.5.regularizer(1): Reading REGULARIZER: gap1.5. Weak regularizer, gaps average 1.5, matches average 10 SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 -207.57 -26.48 -151.19 51.05 40 0 75 @@@@ hmmscore tmp_1-b -i tmp_1-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -26.4115278685381 -Emax 0.0001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.27027027027027 \ -align_short 5 -mdEmax 0.0001 -constraints tmp_1-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(18): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -158.340836 Database has 133 sequences with 18976 residues. @@@@ cp -f tmp_1-b.mult /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.7\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.cst -constraints_out tmp_2-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.a2m (120 sequences, 74 columns) as A2M alignment. @@@@ hmmscore tmp_2-a -i tmp_2-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -simple_threshold -25.7183806877933 -Emax 0.0002 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0002\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.27027027027027 -db prefilter_2.fa -constraints tmp_2-a.cst -constraints_out tmp_2-a-md.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -15.153765 Database has 177 sequences with 63451 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_2-a.mult (28 sequences, 74 columns) as A2M alignment. Reading scores from file tmp_2-a.mstat Writing sequence output to tmp_2-a-sort.a2m. @@@@ cat m0.a2m tmp_2-a-sort.a2m > tmp_2-a.train.seq @@@@ cat m0.cst tmp_2-a-md.cst > tmp_2-a.train.cst # About to count sequences in tmp_2-a.train.seq # num_seqs=148 nll_thresh=-21.7183806877933 frac_id=0.850136584465103 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.850136584465103 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_2-a.train.seq (148 sequences, 74 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 8 (of 148) duplicate sequences with differing IDs Dropping 8 (of 148) duplicate sequences with identical IDs Dropping 13 (of 148) sequences with > 85.0% id 67 sequences left after dropping 81 of 148 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_2-a.train.seq \ -aweight_bits 0.7\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_2-a.train.seq (67 sequences, 74 columns) as A2M alignment. @@@@ buildmodel tmp_2-b -insert tmp_2-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_2-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_2-a.w -constraints tmp_2-a.train.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_1.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 -203.26 -20.43 -130.96 60.73 40 0 75 @@@@ hmmscore tmp_2-b -i tmp_2-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -25.7183806877933 -Emax 0.0002 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.27027027027027 \ -align_short 5 -mdEmax 0.0002 -constraints tmp_2-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(18): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -143.083649 Database has 148 sequences with 30191 residues. @@@@ cp -f tmp_2-b.mult /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.6\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.cst -constraints_out tmp_3-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.a2m (132 sequences, 74 columns) as A2M alignment. @@@@ hmmscore tmp_3-a -i tmp_3-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -simple_threshold -24.1089427738805 -Emax 0.001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.27027027027027 -db prefilter_3.fa -constraints tmp_3-a.cst -constraints_out tmp_3-a-md.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) .. Average NLL-Simple NULL score: -10.446630 Database has 1561 sequences with 562559 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_3-a.mult (47 sequences, 74 columns) as A2M alignment. Reading scores from file tmp_3-a.mstat Writing sequence output to tmp_3-a-sort.a2m. @@@@ cat m0.a2m tmp_3-a-sort.a2m > tmp_3-a.train.seq @@@@ cat m0.cst tmp_3-a-md.cst > tmp_3-a.train.cst # About to count sequences in tmp_3-a.train.seq # num_seqs=167 nll_thresh=-20.1089427738805 frac_id=0.815406698079531 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.815406698079531 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_3-a.train.seq (167 sequences, 74 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 13 (of 167) duplicate sequences with differing IDs Dropping 13 (of 167) duplicate sequences with identical IDs Dropping 23 (of 167) sequences with > 81.5% id 71 sequences left after dropping 96 of 167 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_3-a.train.seq \ -aweight_bits 0.6\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_3-a.train.seq (71 sequences, 74 columns) as A2M alignment. @@@@ buildmodel tmp_3-b -insert tmp_3-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_3-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_3-a.w -constraints tmp_3-a.train.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_2.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 -195.69 -21.34 -105.96 65.87 40 0 75 @@@@ hmmscore tmp_3-b -i tmp_3-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -24.1089427738805 -Emax 0.001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.27027027027027 \ -align_short 5 -mdEmax 0.001 -constraints tmp_3-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(18): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -129.262848 Database has 169 sequences with 43657 residues. @@@@ cp -f tmp_3-b.mult /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.a2m # About to count sequences in prefilter_4.fa @@@@ modelfromalign tmp_4-a -alignfile /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.cst -constraints_out tmp_4-a.cst Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.a2m (144 sequences, 74 columns) as A2M alignment. @@@@ hmmscore tmp_4-a -i tmp_4-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -simple_threshold -22.4995048540528 -Emax 0.005 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.27027027027027 -db prefilter_4.fa -constraints tmp_4-a.cst -constraints_out tmp_4-a-md.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) .................... Average NLL-Simple NULL score: -7.766241 Database has 19087 sequences with 6591740 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_4-a.mult (96 sequences, 74 columns) as A2M alignment. Reading scores from file tmp_4-a.mstat Writing sequence output to tmp_4-a-sort.a2m. @@@@ cat m0.a2m tmp_4-a-sort.a2m > tmp_4-a.train.seq @@@@ cat m0.cst tmp_4-a-md.cst > tmp_4-a.train.cst # About to count sequences in tmp_4-a.train.seq # num_seqs=216 nll_thresh=-18.4995048540528 frac_id=0.761536171984529 @@@@ uniqueseq thinned_tmp -alignfile tmp_4-a.train.seq -a protein \ -percent_id 0.761536171984529 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_4-a.train.seq (216 sequences, 74 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 27 (of 216) duplicate sequences with differing IDs Dropping 27 (of 216) duplicate sequences with identical IDs Dropping 52 (of 216) sequences with > 76.2% id 77 sequences left after dropping 139 of 216 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_4-a.train.seq \ -aweight_bits 0.5\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_4-a.train.seq (77 sequences, 74 columns) as A2M alignment. @@@@ buildmodel tmp_4-b -insert tmp_4-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_4-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/fssp-trained.regularizer -sequence_weights tmp_4-a.w -constraints tmp_4-a.train.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_3.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 -197.63 -21.31 -75.39 63.10 35 0 75 @@@@ hmmscore tmp_4-b -i tmp_4-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -db m0.a2m -db tmp_4-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -22.4995048540528 -Emax 0.005 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.27027027027027 \ -align_short 5 -mdEmax 0.005 -constraints tmp_4-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.cst Reading parameter file tmp_4-b.mod tmp_4-b.mod(18): Reading MODEL -- Final model for run tmp_4-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -109.528923 Database has 218 sequences with 72439 residues. @@@@ cp -f tmp_4-b.mult /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.a2m @@@@ modelfromalign tmp_5-a -alignfile /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.cst -constraints_out tmp_5-a.cst Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.a2m (202 sequences, 74 columns) as A2M alignment. @@@@ hmmscore tmp_5-a -i tmp_5-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 541007 \ -simple_threshold -22.4995048540528 -Emax 0.005 \ -adpstyle 5 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.27027027027027 -db prefilter_4.fa -constraints tmp_5-a.cst -constraints_out tmp_5-a-md.cst Reading parameter file tmp_5-a.mod tmp_5-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k_4.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) .................... Average NLL-Simple NULL score: -7.666042 Database has 19087 sequences with 6591740 residues. @@@@ sortseq tmp_5-a-sort -alignfile tmp_5-a.mult \ -NLLfile tmp_5-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_5-a.mult (64 sequences, 74 columns) as A2M alignment. Reading scores from file tmp_5-a.mstat Writing sequence output to tmp_5-a-sort.a2m. @@@@ cat m0.a2m tmp_5-a-sort.a2m > tmp_5-a.train.seq @@@@ cat m0.cst tmp_5-a-md.cst > tmp_5-a.train.cst @@@@ cp tmp_5-a.train.seq /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k.a2m @@@@ cp tmp_5-a.train.cst /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-beta-21999 < /dev/null gzip -f pf02272-tuned.t2k.a2m pf02272-tuned.t2k_*.a2m prettyalign pf02272-tuned.t2k.a2m.gz -m8 -i -n -L3333 > pf02272-tuned.t2k.pa SAM: prettyalign v3.2 (July 31, 2000) compiled 08/11/00_16:27:51 gunzip -c pf02272-tuned.t2k.a2m.gz > tmp.a2m a2m2html -a2m_in tmp.a2m -retrieve > pf02272-tuned.t2k.pa.html SAM: /projects/compbio/bin/alpha/prettyalign v3.2 (July 31, 2000) compiled 08/11/00_16:27:51 rm tmp.a2m echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net > tmp.script echo ReadA2M pf02272-tuned.t2k.a2m.gz >> tmp.script echo PrintPrediction pf02272-tuned.t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta pf02272-tuned.t2k.2d.seq >> tmp.script echo PrintRDB pf02272-tuned.t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from pf02272-tuned.t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # pf02272-tuned.t2k.a2m with 184 sequences, total weight= 109.229 avg weight= 0.593633 clipped 46 iterations # AdjustWeights couldn't save exactly 1.4 bits/position, saving 1.29973 bits. Regularizing alignment for pf02272-tuned.t2k.a2m.gz # After reading pf02272-tuned.t2k.a2m.gz, have 74 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to pf02272-tuned.t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to pf02272-tuned.t2k.2d.seq # command:# Network initialization done # Printing prediction to pf02272-tuned.t2k.2d.rdb # command:rm tmp.script gunzip -f pf02272-tuned.t2k.a2m.gz /projects/compbio/usr/karplus/src/phytree/phytree -o -i -r flat pf02272-tuned.t2k pf02272-tuned.t2k.a2m /projects/compbio/lib/recode2.20comp Prior library /projects/compbio/lib/recode2.20comp read. Reading alignment file pf02272-tuned.t2k.a2m (184 sequences) as A2M alignment. Alignment pf02272-tuned.t2k.a2m read. Adding sequences:0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 One dot for every 10 merges: .................. Merges done. CPU = user 0: 1:19 system 0: 0: 0 gzip -f pf02272-tuned.t2k.a2m gzip -f pf02272-tuned.t2k_sorted.a2m rm pf02272-tuned.t2k.phytrace pf02272-tuned.t2k.tree_weight prettyalign pf02272-tuned.t2k_sorted.a2m.gz -m8 -i -n -L3333 > pf02272-tuned.t2k_sorted.pa SAM: prettyalign v3.2 (July 31, 2000) compiled 08/11/00_16:27:51 /projects/compbio/usr/karplus/src/phytree/dg pf02272-tuned.t2k.tree /projects/compbio/usr/karplus/src/phytree/dtree pf02272-tuned.t2k.tree make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/pfam-dhha' echo "WeightingRegularizer /projects/compbio/lib/recode3.20comp" > tmp.script echo "SequenceWeight EntropyWeight 0.5 10.0" >> tmp.script echo "ReadA2M pf02272-tuned.t2k.a2m.gz" >> tmp.script echo "SavingsRegularizer /projects/compbio/lib/recode3.20comp" >> tmp.script echo "PrintSavings pf02272-tuned.t2k.saves" >> tmp.script echo "exit" >> tmp.script estimate-dist < tmp.script # command:Weighting regularizer set to recode3.20comp # command:Sequence weighting on input set to EntropyWeight(0.5, 10) # command:Reading A2M format from pf02272-tuned.t2k.a2m.gz % using regularizer recode3.20comp % pf02272-tuned.t2k.a2m.gz with 184 sequences, total weight= 8.08555 avg weight= 0.0439432 After reading pf02272-tuned.t2k.a2m.gz, have 74 columns, totalling 513.629 Using SequenceWeight EntropyWeight(0.5, 10) Using regularizer recode3.20compfor sequence weight regularizer. # command:Savings regularizer set to recode3.20comp # command:% Computing savings using regularizer recode3.20comp Printed 74 columns to pf02272-tuned.t2k.saves # command:rm tmp.script if test -e pf02272-tuned.t2k-logo.labels ;\ then makelogo -b 60 -t pf02272-tuned.t2k -o pf02272-tuned.t2k-logo.eps -l pf02272-tuned.t2k-logo.labels pf02272-tuned.t2k.saves ;\ else makelogo -b 60 -t pf02272-tuned.t2k -o pf02272-tuned.t2k-logo.eps -lf pf02272-tuned.t2k.2d.seq pf02272-tuned.t2k.saves ;\ fi /projects/compbio/experiments/models.97/scripts99/score-target -alignment pf02272-tuned.t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output pf02272-tuned.t2k-w0.5-pdb.rdb PATH=.:/projects/compbio/experiments/models.97/scripts99:/projects/compbio/bin:/projects/compbio/bin/alpha:/projects/compbio/bin/hmmscripts:/projects/compbio/bin/scripts:/sbin:/usr/sbin:/bin:/usr/bin:/usr/local/gnu/bin:/usr/local/share/request/bin:/usr/local/bin @@@@ mkdir /projects/compbio/tmp/score-target-14640 @@@@ mkdir /projects/compbio/tmp/score-target-14640/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-14640/for-scorescript -a2msfile /projects/compbio/tmp/score-target-14640/score-target.a2m \ -buildscript /projects/compbio/bin/scripts/w0.5 -seqfile /projects/compbio/data/pdb/all-protein -Emax 40.0 -viterbi 0 \ -sw_score 2 -output /projects/compbio/tmp/score-target-14640/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-14640/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-14640/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k.a2m.gz /projects/compbio/tmp/score-target-14640/for-scorescript/split-tmp/beta-8974/pf02272-tuned.t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12142 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp -alignfile /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /export/projects/compbio/experiments/casp4/t87/pfam-dhha/pf02272-tuned.t2k.a2m.gz (184 sequences, 74 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp.a2m. Dropping 16 (of 184) duplicate sequences with differing IDs Dropping 16 (of 184) duplicate sequences with identical IDs Dropping 36 (of 184) sequences with > 80.0% id 72 sequences left after dropping 112 of 184 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp.a2m (72 sequences, 74 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12142/tmp.mod /projects/compbio/tmp/score-target-14640/for-scorescript/split-tmp/beta-8974/pf02272-tuned.t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12142 80.0% id 72 sequences left after dropping 112 of 184 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32673/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32673/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32673/tmp.a2m (72 sequences, 74 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32673/tmp.mod pf02272-tuned.t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32673