Software: Hmmer
Description
Hmmer is used for searching sequence databases for sequence homologs, and for making sequence alignments.
Available Versions
| Unspecified: | 3.3.2 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/hmmer and its home page: http://hmmer.org.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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