HMMER biosequence analysis using profile hidden Markov models

Help Contents:

1. Contacting us
2. HMMER3 algorithms
3. Supported target databases
4. Search Parameters
5. Results
6. Application programming interface

HMMER algorithms

The following HMMER algorithms/programs are supported by this server:

• phmmer - used to search one or more query protein sequences against a protein sequence database.
• hmmscan - search protein sequences against collections of profiles, e.g. Pfam. In HMMER2 this was called hmmpfam.
• hmmsearch - used to search one or more profiles against a protein sequence database.
• jackhmmer - iteratively search a query protein sequence, multiple sequence alignment or profile HMM against the target protein sequence database.

Longer term, we will support nhmmer that will enable searches with nucleotide sequences. This software is still under development within the Eddy lab, but is expected to become part of the HMMER software package in the near future.

Other Programs

The following is a brief description of the other programs in the HMMER suite. These are only available from downloaded distributions. However, they are used indirectly when performing the searches on the server.

• hmmalign performs a multiple sequence alignment of all the sequences (usually identified by running an hmmsearch) in the input, by aligning them individually to the profile HMM.
• hmmbuild builds a profile HMM for each multiple sequence alignment in the input multiple sequence alignment file, and saves it to a new file.
• hmmconvert utility converts an input profile file to different HMMER formats.
• hmmfetch retrieves one or more profile HMMs from a profile database (e.g. Pfam).
• hmmpress takes a profile database in standard HMMER3 format and constructs binary compressed data files for hmmscan.
• hmmstat utility prints out a tabular file of summary statistics for each profile.