a2m2html output for 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, 1998.
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:

- T0242 B116, Sulfolobus turreted icosahedral virus
- gi|48697006|ref|YP_025003.1|_1:116 hypothetical protein B116 [Sulfolobus turreted icosahedral virus]
- gi|46360620|gb|AAS89082.1| hypothetical protein B116 [Sulfolobus turreted icosahedral virus]
- gi|22122310|ref|NP_666571.1|_1:112 hypothetical protein [Sulfolobus virus SIRV-2]
- gi|17221384|emb|CAC87312.1| hypothetical protein [Sulfolobus virus SIRV-2]
- gi|22122256|ref|NP_666617.1|_1:112 hypothetical protein [Sulfolobus virus SIRV-1]
- gi|19171556|emb|CAC93984.1| hypothetical protein [Sulfolobus virus SIRV-1]
- gi|45655903|ref|YP_003762.1|_1:111 hypothetical protein AFV1p37 [Acidianus filamentus virus 1]
- gi|37719042|emb|CAD98966.1| hypothetical protein [Acidianus filamentus virus 1]
- gi|16753113|ref|NP_445691.1|_1:109 conserved hypothetical protein [Sulfolobus islandicus filamentous virus]
- gi|16751783|gb|AAL27737.1| conserved hypothetical protein [Sulfolobus islandicus filamentous virus]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MGKVFLTNAFSINMLKEFPTTITIDKLDEEDFCLKLELRLEDGTLINAIGHDSTINLVNTLCGTQ
   2 MGKVFLTNAFSINMLKEFPTTITIDKLDEEDFCLKLELRLEDGTLINAIGHDSTINLVNTLCGTQ
   3 MNKVYLANAFSINMLSKFPIKVTIDKIDRLEFCTNI----DNEEIINAIGHDATIQLINSLCDTK
   4 MNKVYLANAFSINMLTKFPTKVVIDKIDRLEFCENI----DNEDIINSIGHDSTIQLINSLCGTT
   5 MGS-YLLNGFSPAMLASGHSVVFFNQIPDVMLCGALT----SDELVNAIGHKSTINLINRICQTN
   6 M--LYILNSATLP-LKPGKEYVIHAK--ELTIEEAKEL-LENERFISAVGHEATAKMLTNIFDVE


         70        80        90        100        110          
         |         |         |          |          |          
   1 LQKNRVEVKMNEGDEALIIMISQRLEEGKVL.SDKEIKDM.YRQGKISFYEVW....
   2 LQKNRVEVKMNEGDEALIIMISQRLEEGKVL.SDKEIKDM.YRQGKISFYEVW....
   3 LEKNRIEIKLDKNDKLYIIQISQRLEEGKIL.SLEEILKL.YESGKVQFFEIIvd..
   4 FQKNRVEIKLEKEDKLYVVQISQRLEEGKIL.TLEEILKL.YESGKVQFFEIIvd..
   5 LKENRIQVMLQDGDEAFIVVVTERLEEGKVL.SDEEITKM.FEDGKIKIYYARvhs.
   6 IPMNRIQIFLDDGDKLLSIILKTRLEEGKVIkTVEELEQIgYN---IWLFEVVtye.