EMBnet

EMBOSS-GCG comparison


Substitutes for GCG Programs

This table has been adapted from the EMBnet Norway EMBOSS-GCG comparison table.

GCG Program

EMBOSS or Other Alternative

Third-party Package Needed

Direct Alternative

Partial Alternative

ASSEMBLE

 

pasteseq

 

BACKTRANSLATE

backtranseq

   

BESTFIT

water, matcher

   

BLAST

BLAST package

 

BLAST

BREAKUP

splitter

   

CHOPUP

Not needed

   

CODONFREQUENCY

compseq, chips, cusp

   

CODONPREFERENCE

 syco, wobble    

COILSCAN

pepcoil    

COMPARE

dottup, dotmatcher    
COMPOSITION compseq, pepstats    

COMPRESSTEXT

 

shell script

 

COMPTABLE

     

CONSENSUS

prophecy

   

CORRESPOND

codcmp

   

CORRUPT

msbar

   

DATASET

dbiflat, dbiblast, dbigcg

   

DETAB

 

shell tools

 

DISTANCES

PHYLIP package

 

PHYLIP

DIVERGE

PHYLIP package

 

PHYLIP

DOTPLOT

dottup / dotmatcher

   

EXTRACTPEPTIDE

transeq

   

FASTA

FASTA package

 

FASTA3

FASTX

FASTA package

 

FASTA3

FETCH

seqret

   

FIGURE

     

FINDPATTERNS

fuzznuc, fuzzpro

   

FINGERPRINT

     

FRAMEALIGN

wise2

 

Wise2

FRAMES

plotorf, showorf

   

FRAMESEARCH

wise2

 

Wise2

FROM*

seqret

   

GAP

needle

   

GAPSHOW

plotcon

   

GCGTOBLAST

seqret / BLAST package

 

BLAST

GEL*

Staden

MSE

Staden, MSE

GETSEQ

newseq

   

GROWTREE

PHYLIP package, clustalw

 

PHYLIP, CLUSTALW

HELICALWHEEL

pepwheel

   

HTHSCAN

helixturnhelix

   

ISOELECTRIC

iep

   

LINEUP

mse

 

MSE

LISTFILE

gnu utils

   

LOOKUP

srs

 

SRS

LPRINT

gnu utils

   

MAP

restrict , remap

   

MAPPLOT

     

MAPSORT

restrict

   

MEME

meme, pratt

 

MEME 2.3.1 (Embassy) or MEME 3.0, PRATT

MFOLD

mfold

 

MFOLD

MOMENT

pepnet, octanol

   

MOTIFS

patmatmotifs

   

MOTIFSEARCH

profit

   

NAME

Not required

setenv

 

NAMES

infoseq 

showdb

 

NETBLAST

BLAST package: blastcl3

 

NETBLAST

NETFETCH

seqret

   

NOOVERLAP

diffseq

   

OLDDISTANCES

clustalw / PHYLIP package

 

CLUSTALW, PHYLIP

ONECASE

 

shell

 

OVERLAP

supermatcher

   

PAUPDISPLAY

PAUP package

 

PAUP 4

PAUPSEARCH

PAUP package

 

PAUP 4

PEPDATA

getorf

shell and emboss

 

PEPPLOT

pepinfo

   

PEPTIDEMAP

digest

   

PEPTIDESORT

     

PILEUP

clustalw

 

CLUSTALW

PLASMIDMAP

cirdna, lindna

   

PLOTFOLD

     

PLOTSIMILARITY

plotcon

   

PLOTSTRUCTURE

pepinfo

   

PLOTTEST

Not needed

   

PRETTY

cons, prettyplot

   

PRETTYBOX

prettyplot

   

PRIME

eprimer3

 

Primer3

PROFILEGAP

clustalw, prophet

 

CLUSTALW

PROFILEMAKE

prophecy

   

PROFILESCAN

patmatdb

   

PROFILESEARCH

profit

   

PROFILESEGMENTS

     

PUBLISH

seqret, showseq

   

RED

 

tex

 

REFORMAT

seqret

   

REPEAT

equicktandem, etandem, einverted, palindrome

   

REPLACE

sed

   

REVERSE

revseq

   

SAMPLE

extractseq

   

SEG

 

maskseq

 

SEGMENTS

 

matcher

 

SEQED

mse

 

MSE

SEQLAB

 

 

EMBOSS.kaptn+KDE2, Apache+EMBOSS-GUI, Jemboss+JDK+Java_WebStart,
or any other graphical EMBOSS interface

SETKEYS

     

SHIFTOVER

     

SHUFFLE

shuffleseq

   

SIMPLIFY

     

SPEW

 

linux

 

SPSCAN

sigcleave

   

SSEARCH

FASTA package

 

FASTA3

STATPLOT

gnuplot

   

STEMLOOP

palindrome, einverted

   

STRINGSEARCH

textsearch, srs

 

SRS

SYMBOL

     

TERMINATOR

     

TESTCODE

wobble

   

TFASTA

FASTA package

 

FASTA3

TFASTX

FASTA package

 

FASTA3

TO*

seqret

   

TRANSLATE

transeq

   

WINDOW

freak

   

WORDSEARCH

     

XNU

seg, xnu

 

seg


Maintained by: Gábor Tóth.
Last updated: 17 October 2002.