HMMER

Revision as of 18:52, 20 June 2007 by Mauro (Talk | contribs)

HMMER HMMER is a freely distributable implementation of profile HMM software for sequence analysis.

HMMER applications can be searched and launched from the Bioinfo website through the PROGsDB.

Most of HMMER applications can be directly launched by CAPRI.

In the VLS environment, the HMMER package is fully available for command line use in the directory /bioprogs/hmmer.

HMMER available programs are:

hmmalign: Align multiple sequences to a profile HMM.
hmmbuild: Build a profile HMM from a given multiple sequence alignment.
hmmcalibrate: Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches.
hmmemit: Generate sequences probabilistically from a profile HMM.
hmmfetch: Retrieve an HMM from an HMM database
hmmpfam: Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence).
hmmsearch: Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family).

The userguide of HMMER package is available here

For more details about HMMER package, visit the HMMER web site