The HMM2 plugin is a toolkit based on the Sean Eddy’s HMMER2 package.

While working on this plugin we were guided by the following principles:

The current version of UGENE provides user interface for three HMM2 tools: HMM buildHMM calibrate and HMM search.

In the original program the corresponding commands are: “hmmbuild”, “hmmcalibrate” and “hmmsearch”.

To access these tools select the Tools ‣ HMMER2 tools submenu of the program main menu:

     <img src="/wiki/download/attachments/4227683/HMM2.png"/>

We highly recommend reading the original HMMER2 documentation to learn how to use utilities provided by the plugin.

SSE2 algorithm is implemented by Leonid Konyaev, Novosibirsk State University. Use of the SSE2 optimized version of the HMM search algorithm with quad-core CPU gives >30x performance boost when compared with the original single-threaded algorithm (single sequence mode).