Hmmer

Introduction

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

For more information, please check:

BioContainers: https://biocontainers.pro/tools/hmmer

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

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load hmmer/XXXX ### you can run *module avail hmmer* to check all available versions

hmmsearch Nramp.hmm protein.fa > out