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Publications from the HMMER project
nhmmer: DNA Homology Search With Profile HMMs
. T. J. Wheeler, S. R. Eddy.
Bioinformatics
, 29:2487-2489, 2013.
Supplementary material :
[19MB, .tar.gz]
abstract
reprint
Challenges in Homology Search: HMMER3 and Convergent Evolution of Coiled-Coil Regions
. J. Mistry, R. D. Finn, S. R. Eddy, A. Bateman, M. Punta.
Nucleic Acids Research
, 41:e121, 2013.
abstract
reprint
Accelerated profile HMM searches
. S. R. Eddy.
PLoS Comp. Biol.
, 7:e1002195, 2011.
abstract
reprint
HMMER Web Server: Interactive Sequence Similarity Searching
. R. D. Finn, J. Clements, S. R. Eddy.
Nucleic Acids Research
, 39:W29-37, 2011.
abstract
reprint
Hidden Markov Model Speed Heuristic and Iterative HMM Search Procedure
. L. S. Johnson, S. R. Eddy, E. Portugaly.
BMC Bioinformatics
, 11:431, 2010.
Supplementary material :
[Software tarball: hmmer2.5.1.tar.gz]
[Scripts/data tarball: scripts_alns_dbs.tar.gz]
abstract
reprint
A New Generation of Homology Search Tools Based on Probabilistic Inference
. S. R. Eddy.
Genome Inform.
, 23:205-211, 2009.
abstract
reprint
A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation
. S. R. Eddy.
PLoS Comput. Biol.
, 4:e1000069, 2008.
Supplementary material :
[Notes and C source code (.tgz)]
abstract
reprint
Remote Protein Homology Detection Using Hidden Markov Models
.
S. Johnson. PhD Thesis:Washington University School of Medicine, 2006.
reprint
What is a Hidden Markov Model?
. S. R. Eddy.
Nature Biotechnology
, 22:1315-1316, 2004.
abstract
reprint
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
.
R. Durbin, S. R. Eddy, A. Krogh, G. J. Mitchison. Cambridge University Press, 1998.
Profile Hidden Markov Models
. S. R. Eddy.
Bioinformatics
, 14:755-763, 1998.
Download software :
[HMMER]
abstract
reprint
Hidden Markov Models
. S. R. Eddy.
Current Opinion in Structural Biology
, 6:361-365, 1996.
abstract
reprint
Maximum Discrimination Hidden Markov Models of Sequence Consensus
. S. R. Eddy, G. Mitchison, R. Durbin.
Journal of Computational Biology
, 2:9-23, 1995.
abstract
preprint
Multiple Alignment Using Hidden Markov Models
.In:
Proc. Third Int. Conf. Intelligent Systems for Molecular Biology
, 114-120. S. R. Eddy, 1995.
reprint