a2m2html output for file tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1999.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0120-116-210 DNA repair protein XRCC4, human
- gi|4507945|ref|NP_003392.1|_116:210 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_116:210 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_116:210 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_116:210 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|9294200|dbj|BAB02102.1|_167:213 (AB026655) gb|AAC13900.1~gene_id:MXC7.14~similar to unknown protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|9800643|gb|AAF91285.2|AF233528_1 (AF233528) putative double strand break repair protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|3056589|gb|AAC13900.1|_125:171 (AC004255) T1F9.10 [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7294937|gb|AAF50266.1|_159:196 (AE003552) CG3448 gene product [Drosophila melanogaster] (Drosophila melanogaster)

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 VENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
   2 VENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
   3 VENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
   4 VENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
   5 VENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
   6 ----------------------------MRSEAERCLAQ-------GEKLCDEKTEFESATYAKF
   7 ----------------------------MKSEAERCLAQ-------GEKLCDEKTEFENATYAKF
   8 ---------------------------------------------EYEKYVRDSKLKEEELLKKF


         70        80        90     
         |         |         |     
   1 ILVLNEKKTKIRSLHNKLLNAAQEREKDIK
   2 ILVLNEKKTKIRSLHNKLLNAAQEREKDIK
   3 ILVLNEKKTKIRSLHNKLLNAAQEREKDIK
   4 ILVLNEKKTKIRSLHNKLLNAAQEREKDIK
   5 ILVLNEKKTKIRSLHNKLLNAAQEREKDIK
   6 LSVLNAKKAKLRALRDK-------------
   7 LSVLNAKKAKLRAVRDK-------------
   8 LLLLNSKKAHIRDLESQL------------