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.
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