HMMER project

The HMMER project is a collaborative project between the HMMER algorithm developers, led by Sean Eddy at HHMI/Harvard University and the HMMER web service team, lead by Rob Finn at EMBL-EBI. The software is available at hmmer.org.

While the HMMER algorithm developers focus on improving the speed and sensitivity of searches, the HMMER web service team takes these algorithms and deploys them in a production environment to enable optimal performance, given a finite set of resources. The service team also works on ensuring that the underlying HMM and sequences databases are regularly updated and that search results are presented in intuitive visualisations. The web interface is freely accessible, allowing users to perform rapid sequence analyses using the HMMER software suite. The servers allow HMMER to be used to address a wide variety of questions involving sequence function, conservation and evolution.

A paper describing the web server has been published in Nucleic Acids Research. In addition to the human interactive website, we have developed an API that allows simple machine access to the same infrastructure. This should allow relatively large scale analysis to be performed in a timely fashion.


HMMER is supported by

EMBL-EBI EMBL is EMBL-EBI’s parent organisation; it provides core funding for HMMER.
Howard Hughes Medical Institute Howard Hughes Medical Institute supports the Eddy group
Wellcome Trust WT maintains the site at which EMBL-EBI is situtated and provides funding for HMMER.

How to cite

If you have used the HMMER website, please consider citing the following publication that describes this work:

HMMER web server: 2015 update R.D. Finn, J. Clements, W. Arndt, B.L. Miller, T.J. Wheeler, F. Schreiber, A. Bateman and S.R. Eddy Nucleic Acids Research (2015) Web Server Issue 43:W30-W38. 10.1093/nar/gkv397 (PDF)