Emboss

Introduction

Emboss is “The European Molecular Biology Open Software Suite”.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/emboss
Home page: http://emboss.open-bio.org

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

6.6.0

BELL

6.6.0

GAUTSCHI

6.6.0

NEGISHI

6.6.0

SCHOLAR

6.6.0

Commands

  • aaindexextract

  • abiview

  • acdc

  • acdgalaxy

  • acdlog

  • acdpretty

  • acdtable

  • acdtrace

  • acdvalid

  • aligncopy

  • aligncopypair

  • antigenic

  • assemblyget

  • backtranambig

  • backtranseq

  • banana

  • biosed

  • btwisted

  • cachedas

  • cachedbfetch

  • cacheebeyesearch

  • cacheensembl

  • cai

  • chaos

  • charge

  • checktrans

  • chips

  • cirdna

  • codcmp

  • codcopy

  • coderet

  • compseq

  • cons

  • consambig

  • cpgplot

  • cpgreport

  • cusp

  • cutgextract

  • cutseq

  • dan

  • dbiblast

  • dbifasta

  • dbiflat

  • dbigcg

  • dbtell

  • dbxcompress

  • dbxedam

  • dbxfasta

  • dbxflat

  • dbxgcg

  • dbxobo

  • dbxreport

  • dbxresource

  • dbxstat

  • dbxtax

  • dbxuncompress

  • degapseq

  • density

  • descseq

  • diffseq

  • distmat

  • dotmatcher

  • dotpath

  • dottup

  • dreg

  • drfinddata

  • drfindformat

  • drfindid

  • drfindresource

  • drget

  • drtext

  • edamdef

  • edamhasinput

  • edamhasoutput

  • edamisformat

  • edamisid

  • edamname

  • edialign

  • einverted

  • embossdata

  • embossupdate

  • embossversion

  • emma

  • emowse

  • entret

  • epestfind

  • eprimer3

  • eprimer32

  • equicktandem

  • est2genome

  • etandem

  • extractalign

  • extractfeat

  • extractseq

  • featcopy

  • featmerge

  • featreport

  • feattext

  • findkm

  • freak

  • fuzznuc

  • fuzzpro

  • fuzztran

  • garnier

  • geecee

  • getorf

  • godef

  • goname

  • helixturnhelix

  • hmoment

  • iep

  • infoalign

  • infoassembly

  • infobase

  • inforesidue

  • infoseq

  • isochore

  • jaspextract

  • jaspscan

  • jembossctl

  • lindna

  • listor

  • makenucseq

  • makeprotseq

  • marscan

  • maskambignuc

  • maskambigprot

  • maskfeat

  • maskseq

  • matcher

  • megamerger

  • merger

  • msbar

  • mwcontam

  • mwfilter

  • needle

  • needleall

  • newcpgreport

  • newcpgseek

  • newseq

  • nohtml

  • noreturn

  • nospace

  • notab

  • notseq

  • nthseq

  • nthseqset

  • octanol

  • oddcomp

  • ontocount

  • ontoget

  • ontogetcommon

  • ontogetdown

  • ontogetobsolete

  • ontogetroot

  • ontogetsibs

  • ontogetup

  • ontoisobsolete

  • ontotext

  • palindrome

  • pasteseq

  • patmatdb

  • patmatmotifs

  • pepcoil

  • pepdigest

  • pepinfo

  • pepnet

  • pepstats

  • pepwheel

  • pepwindow

  • pepwindowall

  • plotcon

  • plotorf

  • polydot

  • preg

  • prettyplot

  • prettyseq

  • primersearch

  • printsextract

  • profit

  • prophecy

  • prophet

  • prosextract

  • pscan

  • psiphi

  • rebaseextract

  • recoder

  • redata

  • refseqget

  • remap

  • restover

  • restrict

  • revseq

  • runJemboss.sh

  • seealso

  • seqcount

  • seqmatchall

  • seqret

  • seqretsetall

  • seqretsplit

  • seqxref

  • seqxrefget

  • servertell

  • showalign

  • showdb

  • showfeat

  • showorf

  • showpep

  • showseq

  • showserver

  • shuffleseq

  • sigcleave

  • silent

  • sirna

  • sixpack

  • sizeseq

  • skipredundant

  • skipseq

  • splitsource

  • splitter

  • stretcher

  • stssearch

  • supermatcher

  • syco

  • taxget

  • taxgetdown

  • taxgetrank

  • taxgetspecies

  • taxgetup

  • tcode

  • textget

  • textsearch

  • tfextract

  • tfm

  • tfscan

  • tmap

  • tranalign

  • transeq

  • trimest

  • trimseq

  • trimspace

  • twofeat

  • union

  • urlget

  • variationget

  • vectorstrip

  • water

  • whichdb

  • wobble

  • wordcount

  • wordfinder

  • wordmatch

  • wossdata

  • wossinput

  • wossname

  • wossoperation

  • wossoutput

  • wossparam

  • wosstopic

  • xmlget

  • xmltext

  • yank

Module

You can load the modules by:

module load biocontainers
module load emboss

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 emboss on our clusters:

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

module --force purge
module biocontainers emboss

# Your emboss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=emboss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers emboss

# Your emboss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=emboss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers emboss

# Your emboss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=emboss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers emboss

# Your emboss workflow...

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

module --force purge
module biocontainers emboss

# Your emboss workflow...