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.
Rob Finn’s HMMER web services team is expanding. We’re looking for people to apply to two new positions to help Rob and Jody push forward on some important ideas for our services. We’re pushing in the direction of using more phylogenetic information (species trees) as we compute database homology searches and deliver the results — [...]
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.