HMMERHEAD

Intro

HMMs have been proven useful in protein sequence analysis. However, a full search of a sequence database using an HMM is computationally expensive. HMMERHEAD is a software package, incorporated into the HMMER HMM suite, that efficiently filters out most of the unrelated sequences while retaining nearly all related ones.

References

Two posters describe HMMERHEAD. The first version was described in RECOMB 2004: abstract, poster. The current version in RECOMB 2007: abstract, poster. A detailed manuscript is in preparation.

hmmerhead 0.6 Release Notes

Fixed bug causing the hmmsearch to (sometimes) crash when no sequence passed filtering.
In hmmer-2.3.2 + hmmerhead 0.5, debug versions printing debug information to stderr were accidently used. Changed those to the release versions.
Removed a file accidently added to the OBJS list in src/Makefile.in of hmmer 2.5.1

Download

HMMER 2.3.2 + HMMERHEAD 0.6: Latest official HMMER release, plus HMMERHEAD.
HMMER 2.5.2: HMMER 2.5, Steve Johnson's version, featuring improved sensitivity (see Steve's thesis), plus HMMERHEAD.
HMMERHEAD only: for integration into your favorite sequence comparison software.

Contact

Please send any enquiries to elonp-hmmerhead@cs.huji.ac.il