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