(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:
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- T0351 NESG:SR355, Bacillus subtilis, 117 res
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10 20 30 40 50 60
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1 MILYDAIMYKYPNAVSRKDFELRNDGNG..SYIEKWNLRAPLPTQAELETWWEELQKNPPYEPPD
2 MILYDAIMYKYPNAVSRKDFELRNDGNG..SYIEKWNLRAPLPTQAELETWWEELQKNPPYEPPD
3 MNIGEAILFKYPTADPTKDFIVQNNGDGtpSYIAEWNIRAPIPTEAELKTWWEELQSTSAYEPPV
4 MNLALAVKYLFPDAIIGEDFIIRDDGDGrgQYIETWRISAPQPSEKELQEAWENYLENPVTDDPQ
70 80 90 100 110
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1 QVELLAQELSQEKLARKQLEELNKTLGNELSDIKLSLLSLKGDYAELEHHHHHH
2 QVELLAQELSQEKLARKQLEELNKTLGNELSDIKLSLLSLKGDY----------
3 QVDLLARELSQEKLARKQLEELNQTLGSELSKIKLQLLTLQGG-----------
4 LSYTSQQLL---------------KLGREMSSLKLEILALKGEMT---------