Versions

• HMMER3 version 3.0 has been installed into Hippu and  Vuori
  

• HMMER3 version 3.0rc1 has been installed into  Murska

• HMMER 2.3.2 software package is available in Hippu within EMBOSS as an EMBASSY-program
• Optimized version of HMMER 2.3.2 has been installed into Hippu and Murska.

Description

Hidden Markov Models (HMM) are mathematical tools that can be used to describe and analyze related or similar sequence areas. Normally HMM-models are derived from multiple sequence alignments so that they contain position specific information about the probabilities of having certain nucleotides or amino acids in each position of an alignment.

The HMMER package contains tools to create and modify HMM-models, use them to do database searches and extend sequence alignments.

The EMBASSY version of HMMER includes all the functions of the original HMMER 2 program in EMBOSS like format. Database searches with HMM profiles can require very long computing times in normal computers.

HMMER programs

Using HMMER at CSC

• Launch Embster

	module load hmmer

	hmmsearch -h

Pfam database

In Hippu, you can use Pfam_A and Pfam_B databases with HMMER commands. For example comparing protein sequence against a Pfam-A HMM-database can be performed with command:

hmmscan $HMMERDB/Pfam-A.hmm sekvenssi.fasta

With native HMMER, you can speed up the hmmpfam and hmmserach commands by using several processors. The number of processors to be used is indicated with option --cpu number. We recommend that you do not use more than four processors.

hmmscan --cpu 4 $HMMERDB/Pfam-A.hmm protein.fasta > result.txt

Documentation for HMMER

• EHMMER manual pages
  
• HMMER users guide
• HMMER home page