institute for computational biomedicine: HMMER

[ description ]

HMMER is a biological sequence analysis tool using profile hidden Markov models (HMMs).

"Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis."

[ about the method ]

R. Durbin, S. Eddy, A. Krogh, G. Mitchison. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. 1998. Cambridge University Press

S.R. Eddy. Profile hidden Markov models. 1998. Bioinformatics, 14:755-763. [Pubmed]

[ documentation ]

Version 2.3.2 is currently installed in our system. The User Guide provided by the Author and "example usage" excerpted from this User Guide are below.

Example Usage

User Guide

[ availability ]

HMMERlocal installation [ access HMMER]

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]

Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301