Hmmer

Introduction

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

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

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=hmmer       # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load hmmer/XXXX ### Latest version is recommended.