(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html
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:
-
- T0344 Hypothetical protein PF2046, Pyrococcus furiosus, 229 res
-
- gi|18894260|gb|AAL82170.1|_1:176 hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|18978418|ref|NP_579775.1| hypothetical protein PF2046 [Pyrococcus furiosus DSM 3638]
-
- gi|3256453|dbj|BAA29136.1|_3:178 184aa long hypothetical protein [Pyrococcus horikoshii OT3]
-
- gi|33359253|ref|NP_142085.2|_11:186 hypothetical protein PH0067 [Pyrococcus horikoshii OT3]
-
- gi|57159905|dbj|BAD85835.1|_1:176 hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|57641581|ref|YP_184059.1| hypothetical protein TK1646 [Thermococcus kodakarensis KOD1]
-
- gi|5457507|emb|CAB48998.1|_1:178 Hypothetical protein [Pyrococcus abyssi GE5]
- gi|14520292|ref|NP_125767.1| hypothetical protein PAB2293 [Pyrococcus abyssi GE5]
10 20 30 40 50 60
| | | | | |
1 ...MRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEV
2 ...MRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEV
3 mk.MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEI
4 gmkMRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEI
5 ...MRIVAADTGGALLDDAYNPLGLIATVAVLVEKPYRTASLSRVKYADPFNYDMSGRQAIRDEA
6 ...MRIVAADTGGAVLDESLQPIGLISTVAVLVEKPYNTAKEFLVKFSDPYNYDLSGRQAILDEI
70 80 90 100 110 120
| | | | | |
1 LLAIELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEET
2 LLAIELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEET
3 ELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEET
4 ELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEET
5 YLAVELAREVKPDVVHLDSTIGGIEVRKLDEPTIEALGITDRGKEVWKDLSRDLQPLAKKLWEET
6 NLAIELAKRTKPDVVHLDSTLGGIEVRKLDEPTIEALSISDKGKEVWKDLSKDVQPLAKKFWEET
130 140 150 160 170
| | | | |
1 NIEIVAIGKSSVPVRIAEIYAGIYSAKWGIENVEK..EGHLIIGLPRYMEV...
2 NIEIVAIGKSSVPVRIAEIYAGIYSAKWGIENVEK..EGHLIIGLPRYMEVnik
3 GIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKE..KGGLLVGYPGIWRLklr
4 GIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKE..KGGLLVGYPGIWRLklr
5 GIEIIAIGKWSVPVRIAEIYSGIYTAKWAIEYARK..NGKVLVGLPRYMRVdik
6 GIEILAIGKSSVPVRIAEIYSGIFSVKWAIEEVKKghKDHLIIGLPRYMGVeir