From farmer@cse.ucsc.edu Thu Jul 13 20:33:24 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id UAA26557 for Message-Id: <200007131838.LAA28798@beta.cse.ucsc.edu> Subject: T0114(target 99 alignment) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0114.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following is the Target99 alignment in the formats you requested. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-963513505.t99align.a2m' Content-Disposition: attachment; filename="t99-results-963513505.t99align.a2m" >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP RLETITLQKWGSWNPGHIHEILSIRIY >gi|6572453|emb|CAB63113.1|_43:128 (AJ242827) antifungal protein [Streptomyces tendae] mklsvrrslgvatvaaaalaatvvpaaaattspttasaigpt-INRTDCN ENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLS DPRLETITLQKWGSWNPGHIHEILSIRIY --simple mime boundary-- From farmer@cse.ucsc.edu Fri Jul 14 00:01:30 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id AAA31668 for Message-Id: <200007132206.PAA17291@beta.cse.ucsc.edu> Subject: T0114(database hits) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0114.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following are search results using the SAM-T99 method for a sequence query against a database. If there are no hits associated with this output, then your score cutoff was too conservative. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="t99-results-963513505.t99dbhits.txt" The E-value is an estimate of approximately how many sequences would score this well by chance in the database searched. For SAM-T99, E-values less than about 0.01 are roughly equivalent, as sequences that score that well have most likely already been included in the SAM-T99 multiple alignment. Database: PDB (updated Mon Jul 10 11:52:35 2000) Score method: average Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 1qh6A -8.32 5.451 -8.32 5.5 --------- --------- : mol:protein-het length:207 Xylanase 1qh6B -8.32 5.451 -8.32 5.5 --------- --------- : mol:protein-het length:207 Xylanase 1qh7A -8.32 5.451 -8.32 5.5 --------- --------- : mol:protein-het length:207 Xylanase 1qh7B -8.32 5.451 -8.32 5.5 --------- --------- : mol:protein-het length:207 Xylanase 1qtsA -7.72 9.93 --------- --------- -7.72 10 1xnd -6.9 22.53 -6.9 22 --------- --------- : mol:protein length:190 Xylanase (Endo-1,4-Beta-Xylanase) (E.C. 3.2. 1enxA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn 1enxB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn 1redA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1redB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1reeA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1reeB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1refA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1refB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Endo-1,4-Beta-Xylanase II 1xyoA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn 1xyoB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn 1xypA -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn 1xypB -6.45 35.32 -6.45 35 --------- --------- : mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-963513505.t99pairwise.a2m' Content-Disposition: attachment; filename="t99-results-963513505.t99pairwise.a2m" >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1qh6A mol:protein-het length:207 Xylanase xivtdnsignhdgydyefwkdsggsgtmilnhggtfsaqwnnvnnilfrk gkkfnetqthqqvgnmsin------------------------------- -----YGANFQPNGN--AYLCVYGWTVDPLVEYYIVDSWGNWRP------ ------pgatpkgtitvdggtydiyetlrvnqpsikgiatfkqywsvrrs krtsgtisvsnhfrawenlgmnmgkmyevaltvegyqssgsanvysntlr ingnpls >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1qh6B mol:protein-het length:207 Xylanase xivtdnsignhdgydyefwkdsggsgtmilnhggtfsaqwnnvnnilfrk gkkfnetqthqqvgnmsin------------------------------- -----YGANFQPNGN--AYLCVYGWTVDPLVEYYIVDSWGNWRP------ ------pgatpkgtitvdggtydiyetlrvnqpsikgiatfkqywsvrrs krtsgtisvsnhfrawenlgmnmgkmyevaltvegyqssgsanvysntlr ingnpls >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1qh7A mol:protein-het length:207 Xylanase xivtdnsignhdgydyefwkdsggsgtmilnhggtfsaqwnnvnnilfrk gkkfnetqthqqvgnmsin------------------------------- -----YGANFQPNGN--AYLCVYGWTVDPLVEYYIVDSWGNWRP------ ------pgatpkgtitvdggtydiyetlrvnqpsikgiatfkqywsvrrs krtsgtisvsnhfrawenlgmnmgkmyevaltvegyqssgsanvysntlr ingnpls >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1qh7B mol:protein-het length:207 Xylanase xivtdnsignhdgydyefwkdsggsgtmilnhggtfsaqwnnvnnilfrk gkkfnetqthqqvgnmsin------------------------------- -----YGANFQPNGN--AYLCVYGWTVDPLVEYYIVDSWGNWRP------ ------pgatpkgtitvdggtydiyetlrvnqpsikgiatfkqywsvrrs krtsgtisvsnhfrawenlgmnmgkmyevaltvegyqssgsanvysntlr ingnpls >T0114 ------------------MINRTDCNENSYLEIHNnegrdtlcfa----- -NAGTMPVAIYGVNWVESGNNVVTLQF--------QRNL----------- ------------SDPRLETITLQKWGSWNPGHIHEILSIRIY-------- -------------------------------------------------- -------------------------------------------------- ------- >1qtsA mol:protein length:247 Ap-2 Clathrin Adaptor Alpha Subunit (Alpha- GSPGIRLGSSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFY GNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVVNIEC ISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWK QLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAG IIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1xnd mol:protein length:190 Xylanase (Endo-1,4-Beta-Xylanase) (E.C. 3.2. qtigpgtgys---------NGYYYSYWNDGHAGVTYTNGGG---GSFTVN WSNSGNFVAGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsiygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawashgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1enxA mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1enxB mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1redA mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1redB mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1reeA mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1reeB mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1refA mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1refB mol:protein-het length:190 Endo-1,4-Beta-Xylanase II xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1xyoA mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1xyoB mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1xypA mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs >T0114 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY >1xypB mol:protein-het length:190 Molecule: Endo-1,4-Beta-Xylanase II; Syn xtiqpgtgyn---------NGYFYSYWNDGHGGVTYTNG---PGGQFSVN WSNSGNFVGGKGWQ---------------------------------pgt knkvinfsgsynpngnsylsvygwsrnplieyyivenfgtynpstgatkl gevtsdgsvydiyrtqrvnqpsiigtatfyqywsvrrnhrssgsvntanh fnawaqqgltlgtmdyqivavegyfssgsasitvs --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-963513505.t99pairwise.casp.al' Content-Disposition: attachment; filename="t99-results-963513505.t99pairwise.casp.al" PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1qh6_A Y 37 Y 70 G 38 G 71 V 39 A 72 N 40 N 73 W 41 F 74 V 42 Q 75 E 43 P 76 S 44 N 77 G 45 G 78 N 46 N 79 V 49 A 80 T 50 Y 81 L 51 L 82 Q 52 C 83 F 53 V 84 Q 54 Y 85 R 55 G 86 N 56 W 87 L 57 T 88 S 58 V 89 D 59 D 90 P 60 P 91 R 61 L 92 L 62 V 93 E 63 E 94 T 64 Y 95 I 65 Y 96 T 66 I 97 L 67 V 98 Q 68 D 99 K 69 S 100 W 70 W 101 G 71 G 102 S 72 N 103 W 73 W 104 N 74 R 105 P 75 P 106 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1qh6_B Y 37 Y 70 G 38 G 71 V 39 A 72 N 40 N 73 W 41 F 74 V 42 Q 75 E 43 P 76 S 44 N 77 G 45 G 78 N 46 N 79 V 49 A 80 T 50 Y 81 L 51 L 82 Q 52 C 83 F 53 V 84 Q 54 Y 85 R 55 G 86 N 56 W 87 L 57 T 88 S 58 V 89 D 59 D 90 P 60 P 91 R 61 L 92 L 62 V 93 E 63 E 94 T 64 Y 95 I 65 Y 96 T 66 I 97 L 67 V 98 Q 68 D 99 K 69 S 100 W 70 W 101 G 71 G 102 S 72 N 103 W 73 W 104 N 74 R 105 P 75 P 106 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1qh7_A Y 37 Y 70 G 38 G 71 V 39 A 72 N 40 N 73 W 41 F 74 V 42 Q 75 E 43 P 76 S 44 N 77 G 45 G 78 N 46 N 79 V 49 A 80 T 50 Y 81 L 51 L 82 Q 52 C 83 F 53 V 84 Q 54 Y 85 R 55 G 86 N 56 W 87 L 57 T 88 S 58 V 89 D 59 D 90 P 60 P 91 R 61 L 92 L 62 V 93 E 63 E 94 T 64 Y 95 I 65 Y 96 T 66 I 97 L 67 V 98 Q 68 D 99 K 69 S 100 W 70 W 101 G 71 G 102 S 72 N 103 W 73 W 104 N 74 R 105 P 75 P 106 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1qh7_B Y 37 Y 70 G 38 G 71 V 39 A 72 N 40 N 73 W 41 F 74 V 42 Q 75 E 43 P 76 S 44 N 77 G 45 G 78 N 46 N 79 V 49 A 80 T 50 Y 81 L 51 L 82 Q 52 C 83 F 53 V 84 Q 54 Y 85 R 55 G 86 N 56 W 87 L 57 T 88 S 58 V 89 D 59 D 90 P 60 P 91 R 61 L 92 L 62 V 93 E 63 E 94 T 64 Y 95 I 65 Y 96 T 66 I 97 L 67 V 98 Q 68 D 99 K 69 S 100 W 70 W 101 G 71 G 102 S 72 N 103 W 73 W 104 N 74 R 105 P 75 P 106 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1qts_A M 1 C 710 I 2 K 711 N 3 N 712 R 4 N 713 T 5 G 714 D 6 V 715 C 7 L 716 N 8 F 717 E 9 E 718 N 10 N 719 S 11 Q 720 Y 12 L 721 L 13 L 722 E 14 Q 723 I 15 I 724 H 16 G 725 N 17 L 726 N 28 N 733 A 29 L 734 G 30 G 735 T 31 R 736 M 32 M 737 P 33 F 738 V 34 I 739 A 35 F 740 I 36 Y 741 Y 37 G 742 G 38 N 743 V 39 K 744 N 40 T 745 W 41 S 746 V 42 T 747 E 43 Q 748 S 44 F 749 G 45 L 750 N 46 N 751 N 47 F 752 V 48 T 753 V 49 P 754 T 50 T 755 L 51 L 756 Q 52 I 757 F 53 C 758 Q 54 N 767 R 55 L 768 N 56 Q 769 L 57 T 770 S 58 D 794 D 59 F 795 P 60 T 796 R 61 E 797 L 62 A 798 E 63 P 799 T 64 V 800 I 65 L 801 T 66 N 802 L 67 I 803 Q 68 Q 804 K 69 F 805 W 70 R 806 G 71 Y 807 S 72 G 808 W 73 G 809 N 74 T 810 P 75 F 811 G 76 Q 812 H 77 N 813 I 78 V 814 H 79 S 815 E 80 V 816 I 81 K 817 L 82 L 818 S 83 P 819 I 84 I 820 R 85 T 821 I 86 L 822 Y 87 N 823 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xnd N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 Y 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 A 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 G 30 G 31 T 31 G 32 A 35 G 33 I 36 S 34 Y 37 F 35 G 38 T 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 A 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1enx_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1enx_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1red_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1red_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1ree_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1ree_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1ref_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1ref_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xyo_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xyo_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xyp_A N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END PFRMAT AL TARGET T0114 AUTHOR UCSC SAM-T99 Web Server METHOD This pairwise alignment was produced using the SAM-T99 method METHOD METHOD ------------- Citations (SAM, SAM-T99, HMMs) ----------------- METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: METHOD Extension and analysis of the basic method, CABIOS 12:95-107, 1996. METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting METHOD remote protein homologies, Bioinformatics 14(10):846-856, 1999. METHOD A. Krogh et al., Hidden Markov models in computational biology: METHOD Applications to protein modeling, JMB 235:1501-1531, Feb 1994. MODEL 1 PARENT 1xyp_B N 10 N 11 S 11 G 12 Y 12 Y 13 L 13 F 14 E 14 Y 15 I 15 S 16 H 16 Y 17 N 17 W 18 N 18 N 19 E 19 D 20 G 20 G 21 R 21 H 22 D 22 G 23 T 23 G 24 L 24 V 25 C 25 T 26 F 26 Y 27 A 27 T 28 N 28 N 29 A 29 G 30 P 33 P 31 V 34 G 32 A 35 G 33 I 36 Q 34 Y 37 F 35 G 38 S 36 V 39 V 37 N 40 N 38 W 41 W 39 V 42 S 40 E 43 N 41 S 44 S 42 G 45 G 43 N 46 N 44 N 47 F 45 V 48 V 46 V 49 G 47 T 50 G 48 L 51 K 49 Q 52 G 50 F 53 W 51 Q 54 Q 52 TER END --simple mime boundary-- From farmer@cse.ucsc.edu Fri Jul 14 00:05:45 2000 Return-Path: Received: from beta.cse.ucsc.edu (beta.cse.ucsc.edu [128.114.48.15]) by cyborg.bioinfo.pl (8.9.3/8.8.7) with SMTP id AAA31719 for Message-Id: <200007132211.PAA04577@beta.cse.ucsc.edu> Subject: T0114(target 99 secondary structure prediction) MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="simple mime boundary" Apparently-To: T0114.target99@cafasp.bioinfo.pl --simple mime boundary Content-type: text/plain; charset=us-ascii The following is the Target99 secondary structure prediction in the formats you requested. Citation: K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps -------------------------------------------------------- For questions or problems, please see the SAM-T99 FAQ at http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html or email us at sam-info@cse.ucsc.edu --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-963513505.t99secstr.fasta' Content-Disposition: attachment; filename="t99-results-963513505.t99secstr.fasta" >T0114 LLLLLLLLLLLEEEEELLLLLLEEEELLLLLLLEEEEEEEEEELLLLEEEEEEELLLLLLLLLEEEEHLLLLLLLLLEEEEEEEEEL --simple mime boundary Content-type: text/plain; charset=us-ascii; name='t99-results-963513505.t99secstr.casp.ss' Content-Disposition: attachment; filename="t99-results-963513505.t99secstr.casp.ss" PFRMAT SS TARGET T0114 AUTHOR UCSC Target99 server METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET T0114 METHOD Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 9 METHOD 7 10 METHOD 5 9 METHOD 11 3 (1 EHL2 ) METHOD The input amino acid frequencies were determined from METHOD alignment /projects/compbio/tmp/hmm-target99-beta-4290/target-align-4290.a2m METHOD with weighted counts, using EntropyWeight(1.4 bits/column, 10) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 1.86607 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: T0114 METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.beta.5809/model.mod METHOD database_files: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Thu Jul 13 15:08:57 2000 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /projects/compbio/tmp/hmm-target99-beta-4290/target-align-4290.a2m METHOD METHOD guide seq name: T0114 METHOD ###end 0 MODEL 1 M C 0.645 I C 0.562 N C 0.659 R C 0.581 T C 0.576 D C 0.611 C C 0.642 N C 0.676 E C 0.572 N C 0.563 S C 0.447 Y E 0.412 L E 0.477 E E 0.499 I E 0.482 H E 0.373 N C 0.514 N C 0.59 E C 0.668 G C 0.731 R C 0.653 D C 0.609 T E 0.403 L E 0.538 C E 0.53 F E 0.496 A C 0.402 N C 0.529 A C 0.618 G C 0.672 T C 0.544 M C 0.507 P C 0.439 V E 0.599 A E 0.615 I E 0.661 Y E 0.619 G E 0.481 V E 0.483 N E 0.473 W E 0.598 V E 0.573 E E 0.475 S C 0.583 G C 0.713 N C 0.713 N C 0.57 V E 0.542 V E 0.696 T E 0.686 L E 0.674 Q E 0.63 F E 0.601 Q E 0.483 R C 0.397 N C 0.497 L C 0.501 S C 0.652 D C 0.746 P C 0.663 R C 0.53 L C 0.37 E C 0.358 T E 0.437 I E 0.505 T E 0.481 L E 0.412 Q H 0.35 K C 0.375 W C 0.425 G C 0.611 S C 0.636 W C 0.628 N C 0.747 P C 0.707 G C 0.642 H C 0.497 I E 0.367 H E 0.411 E E 0.488 I E 0.538 L E 0.537 S E 0.565 I E 0.581 R E 0.585 I E 0.518 Y C 0.603 END --simple mime boundary--