The HMMER software

HMMER algorithms

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

used to search one or more query protein sequences against a protein sequence database
search protein sequences against collections of profiles, such as Pfam. In HMMER2 this was called hmmpfam
used to search one or more profiles against a protein sequence database
iteratively search a query protein sequence, multiple sequence alignment or profile HMM against the target protein sequence database

This software has been released as part of the HMMER software package (version 3.1)

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

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
builds a profile HMM for each multiple sequence alignment in the input multiple sequence alignment file, and saves it to a new file
utility converts an input profile file to different HMMER formats
retrieves one or more profile HMMs from a profile database
takes a profile database in standard HMMER3 format and constructs binary compressed data files for hmmscan
utility prints out a tabular file of summary statistics for each profile