User's Guide

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Altschul, 1991
Altschul, S. F. (1991).
Amino acid substitution matrices from an information theoretic perspective.
J. Mol. Biol., 219:555-565.

Altschul et al., 1990
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990).
Basic local alignment search tool.
J. Mol. Biol., 215:403-410.

Barrett et al., 1997
Barrett, C., Hughey, R., and Karplus, K. (1997).
Scoring hidden Markov models.
Comput. Applic. Biosci., 13:191-199.

Barton, 1990
Barton, G. J. (1990).
Protein multiple sequence alignment and flexible pattern matching.
Meth. Enzymol., 183:403-427.

Bashford et al., 1987
Bashford, D., Chothia, C., and Lesk, A. M. (1987).
Determinants of a protein fold: Unique features of the globin amino acid sequences.
J. Mol. Biol., 196:199-216.

Durbin et al., 1998
Durbin, R., Eddy, S. R., Krogh, A., and Mitchison, G. J. (1998).
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge UK.

Eddy, 1996
Eddy, S. R. (1996).
Hidden Markov models.
Curr. Opin. Struct. Biol., 6:361-365.

Gribskov et al., 1990
Gribskov, M., Luthy, R., and Eisenberg, D. (1990).
Profile analysis.
Meth. Enzymol., 183:146-159.

Gribskov et al., 1987
Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987).
Profile analysis: Detection of distantly related proteins.
Proc. Natl. Acad. Sci. USA, 84:4355-4358.

Konings and Hogeweg, 1989
Konings, D. and Hogeweg, P. (1989).
Pattern analysis of RNA secondary structure: Similarity and consensus of minimal-energy folding.
J. Mol. Biol., 207:597-614.

Krogh et al., 1994
Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994).
Hidden Markov models in computational biology: Applications to protein modeling.
J. Mol. Biol., 235:1501-1531.

Pearson and Lipman, 1988
Pearson, W. and Lipman, D. (1988).
Improved tools for biological sequence comparison.
Proc. Natl. Acad. Sci. USA, 85:2444-2448.

Rabiner, 1989
Rabiner, L. R. (1989).
A tutorial on hidden Markov models and selected applications in speech recognition.
Proc. IEEE, 77:257-286.

Schneider et al., 1992
Schneider, D., Tuerk, C., and Gold, L. (1992).
Selection of high affinity RNA ligands to the bacteriophage R17 coat protein.
J. Mol. Biol., 228:862-869.

Sjölander et al., 1996
Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I. S., and Haussler, D. (1996).
Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology.
Comput. Applic. Biosci., 12:327-345.

Smith and Waterman, 1981
Smith, T. and Waterman, M. (1981).
Identification of common molecular subsequences.
J. Mol. Biol., 147:195-197.

Sonnhammer et al., 1997
Sonnhammer, E. L., Eddy, S. R., and Durbin, R. (1997).
Pfam: A comprehensive database of protein families based on seed alignments.
Proteins, 28:405-420.

Sonnhammer et al., 1998
Sonnhammer, E. L. L., Eddy, S. R., Birney, E., Bateman, A., and Durbin, R. (1998).
Pfam: Multiple sequence alignments and HMM-profiles of protein domains.
Nucl. Acids Res., 26:320-322.

Taylor, 1986
Taylor, W. R. (1986).
Identification of protein sequence homology by consensus template alignment.
J. Mol. Biol., 188:233-258.

Tuerk and Gold, 1990
Tuerk, C. and Gold, L. (1990).
Systematic evolution of ligands by exponential enrichment.
Science, 249:505-510.

Direct comments and questions to <eddy@genetics.wustl.edu>