HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
As part of this evolution in the HMMER software, we are committed to making the software available to as many scientists as possible. Earlier releases of HMMER were restricted to command line use. To make the software more accessible to the wide scientific community, we now provide servers that allow sequence searches to be performed interactively via the Web.
The HMMER dev team is happy to announce an upgrade release of HMMER3, release 3.1. A beta test version of the code is publicly available as a tarball available for download, or from hmmer.org, where you’ll also find precompiled binary releases for Mac and Linux. HMMER 3.1 includes nhmmer and nhmmscan, programs for DNA/DNA homology [...]
HMMER web server: interactive sequence similarity searching
R.D. Finn, J. Clements, S.R. Eddy
Nucleic Acids Research (2011) Web Server Issue 39:W29-W37. PDF
Accelerated profile HMM searches.
S. R. Eddy.
PLoS Comp. Biol., 7:e1002195, 2011.