3.4

HMMER container

Main tool : HMMER

Code repository: https://github.com/EddyRivasLab/hmmer

Basic information on how to use this tool:

• executables:

  • alimask
  • hmmalign
  • hmmbuild
  • hmmconvert
  • hmmemit
  • hmmfetch
  • hmmlogo
  • hmmpgmd
  • hmmpgmd_shard
  • hmmpress
  • hmmscan
  • hmmsearch
  • hmmsim
  • hmmstat
  • jackhmmer
  • makehmmerdb
  • nhmmer
  • nhmmscan
  • phmmer

• help: -h

• version: -v

• description:

HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs).

Full documentation: http://eddylab.org/software/hmmer/Userguide.pdf

Example commands

# build a profile from an alignment
hmmbuild hmm_file msa_file

# search profile against a sequence database
hmmsearch hmm_file seqs.fa