(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:
-
-
- gi|18894260|gb|AAL82170.1|_166:229 hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|18978418|ref|NP_579775.1| hypothetical protein PF2046 [Pyrococcus furiosus DSM 3638]
-
- gi|5457507|emb|CAB48998.1|_168:231 Hypothetical protein [Pyrococcus abyssi GE5]
- gi|14520292|ref|NP_125767.1| hypothetical protein PAB2293 [Pyrococcus abyssi GE5]
-
- gi|57159905|dbj|BAD85835.1|_166:227 hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|57641581|ref|YP_184059.1| hypothetical protein TK1646 [Thermococcus kodakarensis KOD1]
-
- gi|33359252|ref|NP_877731.1|_1:56 hypothetical protein PH0066.1n [Pyrococcus horikoshii OT3]
10 20 30 40 50 60
| | | | | |
1 ...LIIGLPRYMEVNIKDGKIIGRSLDPREGGLYGSAEVSVPEGVKWEIYPNPVARRFMIFEIFS
2 eghLIIGLPRYMEVNIKDGKIIGRSLDPREGGLYGSAEVSVPEGVKWEIYPNPVARRFMIFEIFS
3 kdhLIIGLPRYMGVEIRDGKITGRTLDPREGNLYGEISIEVPNNIKWEVYPNPLVRRFHIFEIWG
4 ngkVLVGLPRYMRVDIKPGEIYGESLDPREGGLFGKIETNT-DGINWELYPNPLVRRYMVLEVWK
5 ...--------MEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS
1 KR
2 KR
3 EY
4 E-
5 KS