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Abstract: Motivation A new hidden Markov model method #SAM-T98# for #nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model #hmm# from the sequence and homologs found using the hmm for database search. SAM-T98 is also used to construct model libraries automatically from sequences in structural databases. (Update)
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BibTeX entry: (Update)
Kevin Karplus, Christian Barrett, and Richard Hughey. Hidden markov models for detecting remote protein homologies. Bioinformatics, 14(10):846--856, 1998. http://citeseer.ist.psu.edu/karplus99hidden.html More
@misc{ karplus98hidden,
author = "K. Karplus and C. Barrett and R. Hughey",
title = "Hidden markov models for detecting remote protein homologies",
text = "Kevin Karplus, Christian Barrett, and Richard Hughey. Hidden markov models
for detecting remote protein homologies. Bioinformatics, 14(10):846--856,
1998.",
year = "1998",
url = "citeseer.ist.psu.edu/karplus99hidden.html" }
Citations (may not include all citations):266 Gapped BLAST and PSIBLAST: A new generation of protein datab.. - Altschul, Madden et al. - 1997
171 Hidden Markov models in computational biology: Applications .. - Krogh, Brown et al. - 1994
155 Improved tools for biological sequence comparison (context) - Pearson, Lipman - 1988
71 Hidden Markov models of biological primary sequence informat.. (context) - Baldi, Chauvin et al. - 1994
56 Protein structure comparison by alignment of distance matric.. (context) - Holm, Sander - 1993
47 Amino acid substitution matrices from an information theoret.. (context) - Altschul - 1991
46 Hidden Markov models for sequence analysis: Extension and an.. - Hughey, Krogh - 1996
34 Multiple alignment using hidden Markov models (context) - Eddy - 1995
30 Comparison of methods for searching protein sequence databas.. (context) - Pearson - 1995
29 Protein modeling using hidden Markov models: Analysis of glo.. - Haussler, Krogh et al. - 1993
28 Maximum discrimination hidden Markov models of sequence cons.. (context) - Eddy, Mitchison et al. - 1995
24 Sequence comparisons using multiple sequences detect twice a.. (context) - Park, Karplus et al. - 1998
18 Comprehensive assessment of automatic structural alignment a.. - Gerstein, Levitt - 1998
17 Intermediate sequences increase the detection of homology be.. (context) - Park, Teichmann et al. - 1997
16 Scoring hidden Markov models - Barrett, Hughey et al. - 1997
16 Predicting protein structure using hidden Markov models - Karplus, Kimmen et al. - 1997
11 Meta-MEME: Motif-based hidden Markov models of protein famil.. - Grundy, Bailey et al. - 1997
10 Basic local alignment search tool (context) - Altshul, Gish et al. - 1990
8 Weighting hidden Markov models for maximum discrimination - Karchin, Hughey - 1998
8 Dirichlet mixtures: A method for improving detection of weak.. - olander, Karplus et al. - 1996
7 scop: a structural classi#cation of proteins database - Hubbard, Murzin et al. - 1997
7 Position-based sequence weights (context) - Heniko - 1994
7 Parameterization studies for the SAM and HMMER methods of hi.. - McClure, Smith et al. - 1996
6 Reduced space hidden Markov model training - Tarnas, Hughey - 1998
5 Comparative accuracy of methods for protein-sequence similar.. (context) - Agarwal, States - 1998
4 Distributed on the Internet via anonymous FTP from ftp (context) - NRP, Protein - 1998
4 Molecular propinquity: evolutionary and structural relations.. (context) - Brenner - 1996
3 Protein sequence database (context) - Barker, George et al. - 1990
2 le syntax for biomolecular sequence motifs and its function .. (context) - Bucher, Bairoch - 1994
2 exible motif search technique based on generalized pro#les (context) - Bucher, Karplus et al. - 1996
2 The FSSP database: Fold classi#cation based on structure-str.. (context) - Holm, Sander - 1996
2 cation of three-dimensional protein folds (context) - Holm, Sander - 1997
1 PairWise and SearchWise: #nding the optimal alignment is a s.. (context) - Birney, Thompson et al. - 1996
1 Pfam: A comprehensive database of protein families based on .. (context) - Smith, Waterman et al. - 1997
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