HMMER

HMMER

Infobox Software
name = HMMER
developer = Sean Eddy
latest_release_version = 2.3.2
latest_release_date = release date|2003|10|03
programming language = C
language = English
genre = Bioinformatics tool
license = GPL
website = http://hmmer.janelia.org/

HMMER is a free software package for protein sequence analysis [cite book
last = Durbin
first = Richard
coauthors = Sean R. Eddy, Anders Krogh, Graeme Mitchison
title = Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
publisher = Cambridge University Press
date = 1998
location =
isbn = 0521629713] . It is used for sensitive database search using profile-HMMs. The profile-HMMs are based on the work of Krogh and colleagues.cite journal |author=Krogh A, Brown M, Mian IS, Sjölander K, Haussler D |title=Hidden Markov models in computational biology. Applications to protein modeling |journal=J. Mol. Biol. |volume=235 |issue=5 |pages=1501–31 |year=1994 |month=February |pmid=8107089 |doi=10.1006/jmbi.1994.1104 |url=] Basically, HMMER is a console utility ported to every major operating system including different versions of Linux, Windows and Mac OS.

Results achieved during the work on HMMER were the basis for PFAM database creation.

HMMER is integrated into UGENE bioinformatics tool as a plugin.

ee also

*Hidden Markov model
*Sequence alignment software
* PFAM
*UGENE

References


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