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:

- T0460 PF0246, Pyrococcus furiosus, 111 residues
- gi|18976618|ref|NP_577975.1|_1:103 hypothetical protein PF0246 [Pyrococcus furiosus DSM 3638]
- gi|18892185|gb|AAL80370.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14521894|ref|NP_127371.1|_1:102 hypothetical protein PAB1233 [Pyrococcus abyssi GE5]
- gi|5459114|emb|CAB50600.1| Hypothetical protein [Pyrococcus abyssi GE5]
- gi|57641721|ref|YP_184199.1|_1:102 hypothetical protein TK1786 [Thermococcus kodakarensis KOD1]
- gi|57160045|dbj|BAD85975.1| hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|14591662|ref|NP_143749.1|_1:102 hypothetical protein PH1920 [Pyrococcus horikoshii OT3]
- gi|3258362|dbj|BAA31045.1| 102aa long hypothetical protein [Pyrococcus horikoshii OT3]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MNSEVIKEFLEDIGEDYIELENEIHLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKY
   2 MNSEVIKEFLEDIGEDYIELENEIHLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKY
   3 MNSEVIKEFLEDIGADYIELEGEIHLEPRVFYEVWKYVGEPELKTYVVEDEVVEPGEYDPPEMKY
   4 MHFEVVKEFLEDIGADWIEIEGEIHLDPEVFYEVWKYVGQPELKTYVIEDEVVEPGSYDPPEMKY
   5 MNSEVIKEFLEDIGADYIELEGEIHLEPKVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMRY


         70        80        90       100       110 
         |         |         |         |         | 
   1 TNVKKVKIKKVYFETLDNVRVVTDYSEFQKILKKRGTKLEHHHHHH
   2 TNVKKVKIKKVYFETLDNVRVVTDYSEFQKILKKRGTK--------
   3 TEARKIKIKKVYFETLDGVKVVTDYSDFQKILKETKA---------
   4 TDVKKVKIKKVYFETLDGKKIVTDYSEFQKLVKEKSA---------
   5 TEAKKIKIKKVYFETLDGVKVVTDHSEFQKIIKEMKS---------