HMM3¶
The HMM3 plugin is a toolkit based on the 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 graphical interface for all supported utilities for most of the platforms.
- Be compatible with the original HMMER3 package.
- Create the high-performance solution utilizing modern multi-core processors.
The current version of UGENE provides 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 ‣ HMMER3 tools submenu of the program main menu:
We highly recommend reading the original HMMER3 documentation to learn how to use utilities provided by the plugin.
Building HMM Model (HMM3 Build)¶
The HMM3 build tool is used to build a new HMM profile from a multiple alignment. You can use any alignment file formats supported by UGENE.
The output HMM profile format is compatible with the HMMER3 package, but it is not compatible with the HMMER2.
The HMM3 build automatically calibrates the target model.
The HMM3 configuration dialog provides an easy way to set appropriate search parameters.
Here you can see effective weighting strategies options:
Searching Sequence Using HMM Profile (HMM3 Search)¶
The HMM3 search tool reads a HMM profile from a file and searches a sequence for significantly similar sequence matches.
The sequence must be selected in the Project view or there must be an active Sequence view window opened.
If the selected sequence is nucleic and profile HMM is built from amino alignment, the sequence will be automatically translated and searched in all possible frames (6 totally).
If a profile HMM is built for nucleic alignment, the search is performed for both strands (direct and complement).
The HMM3 search accepts the HMMER2 HMM profiles (amino only) as a backward compatibility feature. An interesting post about using the HMMER2 models with the HMMER3 is available on the Sean Eddy’s blog.
For example, reporting thresholds options can be configured using the dialog:
The search results are stored as sequence annotations in the Genbank file format.
Warning
The HMM3 search works only with files that contain a single HMM model.
Searching Sequence Against Sequence Database (Phmmer Search)¶
The Phmmer search tool searches for query sequence matches in sequence database, much as BLASTP or FASTA would do.
The Phmmer search works essentially like the HMM3 search does, except you provide a query sequence instead of a query profile HMM.
The database sequence must be selected in the Project view or there must be an active Sequence view window opened.
Select the query sequence in the Phmmer search dialog:
You can set options of the Phmmer search by choosing the needed dialog tab. Here you can see the e-value calibration options:
The results are stored as sequence annotations in the Genbank file format.
Warning
The Phmmer search works only with single-sequence databases.