HMM3

The HMM3 plugin is a toolkit based on Sean Eddy’s HMMER3 package.

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

• Make the HMMER3 tools accessible to a wider user audience by providing a graphical interface for all supported utilities on most platforms.
• Ensure compatibility with the original HMMER3 package.
• Create a high-performance solution utilizing modern multi-core processors.

The current version of UGENE provides a user interface for three HMM3 tools: HMM3 build, HMM3 search, and Phmmer search.

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

To access these tools, select the Tools ‣ HMMER tools submenu of the program’s main menu:

We highly recommend reading the original HMMER3 documentation to learn how to use the utilities provided by the plugin.

• Building HMM Model
• Sequence Search Using HMM Profile
• Searching Sequence Against Sequence Database