HMM3 plugin

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 HMMER 3 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 HMMER 3 package.
  
  
• Create the high-performance solution utilizing modern multicore processors.
  
  

The current version of Unipro UGENE provides the user interface for three HMM3 tools: hmmbuild, hmmsearch and phmmer.

To access these tools select "Tools->HMM3 (Hidden Markov models)" submenu in the main program menu.

We highly recommend reading the original HMMER 3 documentation to learn how to use utilities provided by the plugin.


Building HMM model (hmmbuild):

'Hmmbuild' 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 HMMER 3 package, but not compatible with HMMER 2.

'Hmmbuild' automatically calibrates the target model.

HMM3 configuration dialog provides an easy way to set appropriate search parameters.
Here you can see an effective weighting strategies options:

'Hmmsearch' tool reads a HMM profile from file and searches sequence for significantly similar sequence matches.

The sequence must be selected in '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 total).

If a profile HMM is built for nucleic alignment, the search is performed for both direct and complement strands.

'hmmsearch' accepts HMMER 2 HMM profiles (amino only) as a backward compatibility feature.
An interesting post about using HMMER 2 models with HMMER 3 is available on Sean Eddy's blog.

Reporting tresholds options can be configured using a fancy dialog:

The search results are stored as sequence annotations in Genbank file format.

'phmmer' searches for query sequence matches in sequence database, much as BLASTP or FASTA would do.

'phmmer' works essentially like 'hmmsearch' does, except you provide a query sequence instead of a query profile HMM.

Database sequence must be selected in 'Project' view or there must be active sequence view window opened.

User selects query sequence in 'phmmer' dialog:

You can set options of 'phmmer' by chosing needed dialog tab.
Here you can see e-value calibration options:

The results are stored as sequence annotations in Genbank file format (like 'hmmsearch' does).

• HMM3 availability for UGENE Workflow designer.
  
  
• Complete support for search with PFAM databases for 'hmmsearch'.
  
  
• Support for HMMER 3 'jackhmmer' tool: single sequence query iterative search.
  
  
• High-performance solutions for HMM3 tools (distributed computing, GPGPU, SIMD).