HMMER project background

The HMMER project is a Howard Hughes Medical Institute visiting project, hosted at HHMI Janelia Farm Research Campus. The project team currently consists of Rob Finn and Jody Clements, who are affiliated to the Scientific Computing department. In collaboration with the Eddy-Rivaslaboratory, the aim is to provided state-of-the-art, freely accessible web interfaces and services to allow users to perform rapid sequence analysis using the HMMER3 software suite. The servers should allow HMMER3 to be applied to a wide variety of questions concerning sequence function, conservation and evolution.

The early releases of the website have focuses on providing a simple interface, with the introduction of mechanisms for interrogating and refining search results based on different criteria, such as taxonomy or domain architectures. The current version of the website is 1.1. 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.

For specific questions about the Web server, please contact the Web server project team leader, Rob Finn, for questions about the HMMER3 code, contact the HMMER3 project leader, Sean Eddy. For general questions about using HMMER or these servers, please using the HMMER mailing list.