Emboss

Introduction

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

For more information, please check its website: https://biocontainers.pro/tools/emboss and its home page: http://emboss.open-bio.org.

Versions

• 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 -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
ml biocontainers emboss