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:

- T0125 Sp18 protein, Haliotis fulgens
- gi|604529|gb|AAC37232.1|_18:158 (L36589) fertilization protein [Haliotis fulgens] (Haliotis fulgens)
- gi|1097391|prf||2113425D fusagenic protein [Haliotis fulgens] (Haliotis fulgens)
- gi|604531|gb|AAC37233.1|_26:165 (L36590) fertilization protein [Haliotis corrugata] (Haliotis corrugata)
- gi|1097392|prf||2113425E fusagenic protein [Haliotis corrugata] (Haliotis corrugata)
- gi|604527|gb|AAC37230.1|_21:148 (L36553) fertilization protein [Haliotis sorenseni] (Haliotis sorenseni)
- gi|1097389|prf||2113425B fusagenic protein [Haliotis sorenseni] (Haliotis sorenseni)
- gi|604525|gb|AAC37229.1|_22:148 (L36552) fertilization protein [Haliotis rufescens] (Haliotis rufescens)
- gi|1097388|prf||2113425A fusagenic protein [Haliotis rufescens] (Haliotis rufescens)
- gi|604533|gb|AAC37231.1|_22:148 (L36554) fertilization protein [Haliotis assimilis] (Haliotis assimilis)
- gi|1097390|prf||2113425C fusagenic protein [Haliotis assimilis] (Haliotis assimilis)

              10        20        30         40        50        60    
              |         |         |          |         |         |    
   1 FDDVVVSRQEQSYVQRGMVNFLDEEMHKLVKRF.RDMRWNLGPGFVFLLKKVNRERMMRYCMDYA
   2 FDDVVVSRQEQSYVQRGMVNFLDEEMHKLVKRF.RDMRWNLGPGFVFLLKKVNRERMMRYCMDYA
   3 WGKIVVKEKNKAAMKIGFMEYLDAKLVKFKRHWlVGANWKLQKFETDEMRYLAIKRLIKVCHGYT
   4 ---TTVSKENAAAMKIAMIKFLDARAGKFKKRV.ENMGYPITPPQWTTLLYYNRQRLMEWCHTYV
   5 ----TVSKENAAAMKVAMIKFLDSRTDRFKKRI.EKIGYPITPPQYTTLLYYNRERLMDWCHNYV
   6 ----SVSKENEAAMKVAMMKFLDMKAGVFKEII.EDMGYPITPPQWTTLLYYNRERLIEFCRSFL


          70        80        90       100       110       120       13
          |         |         |         |         |         |         
   1 RYSKKILQLKHLPVNKKTLTKMGRFVGYRNYGVIRELYADVFRDVQGFRGPKMTAAMRKYSSKDP
   2 RYSKKILQLKHLPVNKKTLTKMGRFVGYRNYGVIRELYADVFRDVQGFRGPKMTAAMRKYSSKDP
   3 IWSQRLIMLKYRPLNEKYFKKVGRYLAWRNYLIVFRMWIGVLK--KNLKRSEITKPMQKLLDTKD
   4 EFSKKIILMGGNKLNKKNFTRMGRIIGWKNQWVLKRRQWEMVR---VMRRYKSTAIAKKIVAMKV
   5 EVSKKIILLGGNKLNKKNFARMGRIIGWKNQWILKRRQWHMVR---VMRRYKASAIAKKIVAMKV
   6 ALSKKIILLGGNKLNKANFARMGRILGWKSQWAVRQRQWGMVR---VSRRHTSTAIAKRIVAMKV


      0       140 
     |         | 
   1 GTFPCKNEKRRG
   2 GTFPCKNEKRRG
   3 GELPCPVRKIHG
   4 ADLPC-------
   5 ADLPC-------
   6 ADLPC-------