Hmmer

Introduction

Hmmer is used for searching sequence databases for sequence homologs, and for making sequence alignments.

For more information, please check its website: https://biocontainers.pro/tools/hmmer and its home page: http://hmmer.org.

Versions

  • 3.3.2

Commands

  • alimask

  • easel

  • esl-afetch

  • esl-alimanip

  • esl-alimap

  • esl-alimask

  • esl-alimerge

  • esl-alipid

  • esl-alirev

  • esl-alistat

  • esl-compalign

  • esl-compstruct

  • esl-construct

  • esl-histplot

  • esl-mask

  • esl-mixdchlet

  • esl-reformat

  • esl-selectn

  • esl-seqrange

  • esl-seqstat

  • esl-sfetch

  • esl-shuffle

  • esl-ssdraw

  • esl-translate

  • esl-weight

  • hmmalign

  • hmmbuild

  • hmmconvert

  • hmmemit

  • hmmfetch

  • hmmlogo

  • hmmpgmd

  • hmmpgmd_shard

  • hmmpress

  • hmmscan

  • hmmsearch

  • hmmsim

  • hmmstat

  • jackhmmer

  • makehmmerdb

  • nhmmer

  • nhmmscan

  • phmmer

Module

You can load the modules by:

module load biocontainers
module load hmmer

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Hmmer on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hmmer

hmmsearch Nramp.hmm protein.fa > out