2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

HMMER

HMMER is a package of nine programs that use Hidden Markov models (HMMs) for sequence database searching. These HMMs are similar to ``profiles'', ``flexible patterns'', and``templates''. But HMMs have a more consistent probabilistic basis. HMMs are a slight improvement over a carefully constructed profile -- but far less skill and manual intervention is necessary to train a good HMM and use it.

The software is from Sean Eddy, Washington U. His group has a useful homepage.

On-line documentation is available locally.

Man pages are available locally for the following programs:

alistat, getseq, hmmalign, hmmbuild, hmmcalibrate, hmmconvert, hmmemit, hmmer, hmmfetch, hmmindex, hmmpfam, hmmsearch, seqstat, sreformat

Files for the tutorials and demos in the documentation are in /srv/local/hmmercurrent/Demos/ in the CSB core cluster.

Currently HMMER is installed for DEC Alpha's (SGI coming soon).

To get started in the CSB core, type:

setup hmmer (or source /srv/local/setup/hmmer.set)

You then have the above programs in your path.