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:

- T0343 Hypothetical protein PF0280, Pyrococcus furiosus, 104 res
- gi|18892224|gb|AAL80404.1|_1:104 hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|18976652|ref|NP_578009.1| hypothetical protein PF0280 [Pyrococcus furiosus DSM 3638]
- gi|5459081|emb|CAB50567.1|_1:104 Hypothetical protein [Pyrococcus abyssi GE5]
- gi|14521861|ref|NP_127337.1| hypothetical protein PAB1090 [Pyrococcus abyssi GE5]
- gi|57160364|dbj|BAD86294.1|_1:100 hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|57642040|ref|YP_184518.1| hypothetical protein TK2105 [Thermococcus kodakarensis KOD1]

              10        20        30          40        50         60  
              |         |         |           |         |          |  
   1 MTWREILRKEGFLDLGEFIVELVYIDCPCEPIP..PTLAIYDKKGDEWYKVEEA.PNVQNYREAV
   2 MTWREILRKEGFLDLGEFIVELVYIDCPCEPIP..PTLAIYDKKGDEWYKVEEA.PNVQNYREAV
   3 MEWKEKFKREGFLDVGDFIIELIYVDCPCEPLP..PMLAIYDKKEDEWYRVDER.VEANNYTEAF
   4 MNWKKQLREDGYLEIQGFRIELT-LDNTFLDLDyiPRIIVYDEKTSRWYVLRNPiPKGKTLEENW


            70        80        90       100    
            |         |         |         |    
   1 EWAIEVLERIRDGENVKLVSLDGPAPPKVMKRLSLALQKLTE
   2 EWAIEVLERIRDGENVKLVSLDGPAPPKVMKRLSLALQKLTE
   3 EWACSVIERIIRGDNVSLVSIDGPAPDPVLKRLRENLSKLTS
   4 DNAVEVLEMIVKGEIEPNLG-DEDVSNRFLRVLKRNLL----