Program name

Description

aaindexextract

Extract data from AAINDEX

abiview

Reads ABI file and display the trace

acdc

ACD compiler

acdpretty

ACD pretty printing utility

acdtable

Creates an HTML table from an ACD file

acdtrace

ACD compiler on-screen trace

acdvalid

ACD file validation

antigenic

Finds antigenic sites in proteins

backtranambig

Back translate a protein sequence to ambiguous codons

backtranseq

Back translate a protein sequence

banana

Bending and curvature plot in B-DNA

biosed

Replace or delete sequence sections

btwisted

Calculates the twisting in a B-DNA sequence

cai

CAI codon adaptation index

chaos

Create a chaos game representation plot for a sequence

charge

Protein charge plot

checktrans

Reports STOP codons and ORF statistics of a protein

chips

Codon usage statistics

cirdna

Draws circular maps of DNA constructs

codcmp

Codon usage table comparison

codcopy

Reads and writes a codon usage table

coderet

Extract CDS, mRNA and translations from feature tables

compseq

Count composition of dimer/trimer/etc words in a sequence

cons

Creates a consensus from multiple alignments

cpgplot

Plot CpG rich areas

cpgreport

Reports all CpG rich regions

cusp

Create a codon usage table

cutgextract

Extract data from CUTG

cutseq

Removes a specified section from a sequence

dan

Calculates DNA RNA/DNA melting temperature

dbiblast

Index a BLAST database

dbifasta

Database indexing for fasta file databases

dbiflat

Index a flat file database

dbigcg

Index a GCG formatted database

dbxfasta

Database b+tree indexing for fasta file databases

dbxflat

Database b+tree indexing for flat file databases

dbxgcg

Database b+tree indexing for GCG formatted databases

degapseq

Removes gap characters from sequences

descseq

Alter the name or description of a sequence

diffseq

Find differences between nearly identical sequences

digest

Protein proteolytic enzyme or reagent cleavage digest

distmat

Creates a distance matrix from multiple alignments

dotmatcher

Displays a thresholded dotplot of two sequences

dotpath

Non-overlapping wordmatch dotplot of two sequences

dottup

Displays a wordmatch dotplot of two sequences

dreg

Regular expression search of a nucleotide sequence

edialign

Local multiple alignment of sequences

einverted

Finds DNA inverted repeats

embossdata

Finds or fetches data files read by EMBOSS programs

embossversion

Writes the current EMBOSS version number

emma

Multiple alignment program - interface to ClustalW program

emowse

Protein identification by mass spectrometry

entret

Reads and writes (returns) flatfile entries

epestfind

Finds PEST motifs as potential proteolytic cleavage sites

eprimer3

Picks PCR primers and hybridization oligos

equicktandem

Finds tandem repeats

est2genome

Align EST and genomic DNA sequences

etandem

Looks for tandem repeats in a nucleotide sequence

extractfeat

Extract features from a sequence

extractseq

Extract regions from a sequence

extractalign

Extract regions from a sequence alignment

findkm

Find Km and Vmax for an enzyme reaction

freak

Residue/base frequency table or plot

fuzznuc

Nucleic acid pattern search

fuzzpro

Protein pattern search

fuzztran

Protein pattern search after translation

garnier

Predicts protein secondary structure

geecee

Calculates fractional GC content of nucleic acid sequences

getorf

Finds and extracts open reading frames (ORFs)

helixturnhelix

Report nucleic acid binding motifs

hmoment

Hydrophobic moment calculation

iep

Calculates the isoelectric point of a protein

infoalign

Information on a multiple sequence alignment

infoseq

Displays some simple information about sequences

isochore

Plots isochores in large DNA sequences

lindna

Draws linear maps of DNA constructs

listor

Write a list file of the logical OR of two sets of sequences

makenucseq

Creates random nucleotide sequences

makeprotseq

Creates random protein sequences

marscan

Finds MAR/SAR sites in nucleic sequences

maskfeat

Mask off features of a sequence

maskseq

Mask off regions of a sequence

matcher

Finds the best local alignments between two sequences

megamerger

Merge two large overlapping nucleic acid sequences

merger

Merge two overlapping sequences

msbar

Mutate sequence beyond all recognition

mwcontam

Shows molwts that match across a set of files

mwfilter

Filter noisy molwts from mass spec output

needle

Needleman-Wunsch global alignment

newcpgreport

Report CpG rich areas

newcpgseek

Reports CpG rich regions

newseq

Type in a short new sequence

noreturn

Removes carriage return from ASCII files

notseq

Exclude a set of sequences and write out the remaining ones

nthseq

Writes one sequence from a multiple set of sequences

octanol

Displays protein hydropathy

oddcomp

Find protein sequence regions with a biased composition

palindrome

Looks for inverted repeats in a nucleotide sequence

pasteseq

Insert one sequence into another

patmatdb

Search a protein sequence with a motif

patmatmotifs

Search a PROSITE motif database with a protein sequence

pepcoil

Predicts coiled coil regions

pepinfo

Plots simple amino acid properties in parallel

pepnet

Displays proteins as a helical net

pepstats

Protein statistics

pepwheel

Shows protein sequences as helices

pepwindow

Displays protein hydropathy

pepwindowall

Displays protein hydropathy of a set of sequences

plotcon

Plot quality of conservation of a sequence alignment

plotorf

Plot potential open reading frames

polydot

Displays all-against-all dotplots of a set of sequences

preg

Regular expression search of a protein sequence

prettyplot

Displays aligned sequences, with colouring and boxing

prettyseq

Output sequence with translated ranges

primersearch

Searches DNA sequences for matches with primer pairs

printsextract

Extract data from PRINTS

profit

Scan a sequence or database with a matrix or profile

prophecy

Creates matrices/profiles from multiple alignments

prophet

Gapped alignment for profiles

prosextract

Build the PROSITE motif database for use by patmatmotifs

pscan

Scans proteins using PRINTS

psiphi

Phi and psi torsion angles from protein coordinates

rebaseextract

Extract data from REBASE

recoder

Remove restriction sites but maintain same translation

redata

Search REBASE for enzyme name, references, suppliers etc

remap

Display sequence with restriction sites, translation etc

restover

Find restriction enzymes producing specific overhang

restrict

Finds restriction enzyme cleavage sites

revseq

Reverse and complement a sequence

seealso

Finds programs sharing group names

seqmatchall

All-against-all comparison of a set of sequences

seqret

Reads and writes (returns) sequences

seqretsplit

Reads and writes (returns) sequences in individual files

showalign

Displays a multiple sequence alignment

showdb

Displays information on the currently available databases

showfeat

Show features of a sequence

showorf

Pretty output of DNA translations

showseq

Display a sequence with features, translation etc

shuffleseq

Shuffles a set of sequences maintaining composition

sigcleave

Reports protein signal cleavage sites

silent

Silent mutation restriction enzyme scan

sirna

Finds siRNA duplexes in mRNA

sixpack

Display a DNA sequence with 6-frame translation and ORFs

skipseq

Reads and writes (returns) sequences, skipping first few

splitter

Split a sequence into (overlapping) smaller sequences

stretcher

Finds the best global alignment between two sequences

stssearch

Search a DNA database for matches with a set of STS primers

supermatcher

Match large sequences against one or more other sequences

syco

Synonymous codon usage Gribskov statistic plot

tcode

Fickett TESTCODE statistic to identify protein -coding DNA

textsearch

Search sequence documentation. Slow, use SRS and Entrez!

tfextract

Extract data from TRANSFAC

tfm

Displays a program's help documentation manual

tfscan

Scans DNA sequences for transcription factors

tmap

Displays membrane spanning regions

tranalign

Align nucleic coding regions given the aligned proteins

transeq

Translate nucleic acid sequences

trimest

Trim poly-A tails off EST sequences

trimseq

Trim ambiguous bits off the ends of sequences

twofeat

Finds neighbouring pairs of features in sequences

union

Reads sequence fragments and builds one sequence

vectorstrip

Strips out DNA between a pair of vector sequences

water

Smith-Waterman local alignment

whichdb

Search all databases for an entry

wobble

Wobble base plot

wordcount

Counts words of a specified size in a DNA sequence

wordfinder

Match large sequences against one or more other sequences

wordmatch

Finds all exact matches of a given size between 2 sequences

wossname

Finds programs by keywords in their one-line documentation

yank

Reads a sequence range, appends the full USA to a list file