ACD

Program name Description
acdc Test an application ACD file
acdpretty Correctly reformat an application ACD file
acdtable Generate an HTML table of parameters from an application ACD file
acdtrace Trace processing of an application ACD file (for testing)
acdvalid Validate an application ACD file

ALIGNMENT

Program name Description
extractalign Extract regions from a sequence alignment

ALIGNMENT CONSENSUS

Program name Description
cons Create a consensus sequence from a multiple alignment
consambig Create an ambiguous consensus sequence from a multiple alignment
megamerger Merge two large overlapping DNA sequences
merger Merge two overlapping sequences

ALIGNMENT DIFFERENCES

Program name Description
diffseq Compare and report features of two similar sequences

ALIGNMENT DOT PLOTS

Program name Description
dotmatcher Draw a threshold dotplot of two sequences
dotpath Draw a non-overlapping wordmatch dotplot of two sequences
dottup Displays a wordmatch dotplot of two sequences
polydot Draw dotplots for all-against-all comparison of a sequence set

ALIGNMENT GLOBAL

Program name Description
est2genome Align EST sequences to genomic DNA sequence
needle Needleman-Wunsch global alignment of two sequences
needleall Many-to-many pairwise alignments of two sequence sets
stretcher Needleman-Wunsch rapid global alignment of two sequences

ALIGNMENT LOCAL

Program name Description
matcher Waterman-Eggert local alignment of two sequences
seqmatchall All-against-all word comparison of a sequence set
supermatcher Calculate approximate local pair-wise alignments of larger sequences
water Smith-Waterman local alignment of sequences
wordfinder Match large sequences against one or more other sequences
wordmatch Finds regions of identity (exact matches) of two sequences

ALIGNMENT MULTIPLE

Program name Description
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
infoalign Display basic information about a multiple sequence alignment
plotcon Plot conservation of a sequence alignment
prettyplot Draw a sequence alignment with pretty formatting
showalign Display a multiple sequence alignment in pretty format
tranalign Generate an alignment of nucleic coding regions from aligned proteins

ASSORTED

Program name Description
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DATA RESOURCES

Program name Description
cachedas Generates server cache file for DAS servers or for the DAS registry
cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch Generates server cache file for EB-eye search domains
cacheensembl Generates server cache file for an Ensembl server
dbtell Display information about a public database
servertell Display information about a public server
showdb Displays information on configured databases
showserver Displays information on configured servers

DATA RETRIEVAL

Program name Description
codcopy Copy and reformat a codon usage table
seqret Reads and writes (returns) sequences

DATA RETRIEVAL CHEMISTRY DATA

Program name Description
infobase Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue

DATA RETRIEVAL FEATURE DATA

Program name Description
featcopy Reads and writes a feature table

DATA RETRIEVAL ONTOLOGY DATA

Program name Description
edamdef Find EDAM ontology terms by definition
edamhasinput Find EDAM ontology terms by has_input relation
edamhasoutput Find EDAM ontology terms by has_output relation
edamisformat Find EDAM ontology terms by is_format_of relation
edamisid Find EDAM ontology terms by is_identifier_of relation
edamname Find EDAM ontology terms by name
godef Find GO ontology terms by definition
goname Find GO ontology terms by name
ontoget Get ontology term(s)
ontogetcommon Get common ancestor for terms
ontogetdown Get ontology term(s) by parent id
ontogetobsolete Get ontology ontology terms
ontogetroot Get ontology root terms by child identifier
ontogetsibs Get ontology term(s) by id with common parent
ontogetup Get ontology term(s) by id of child
ontoisobsolete Report whether an ontology term id is obsolete
ontotext Get ontology term(s) original full text

DATA RETRIEVAL RESOURCE DATA

Program name Description
drfinddata Find public databases by data type
drfindformat Find public databases by format
drfindid Find public databases by identifier
drfindresource Find public databases by resource
drget Get data resource entries
drtext Get data resource entries complete text

DATA RETRIEVAL SEQUENCE DATA

Program name Description
abiview Display the trace in an ABI sequencer file
coderet Extract CDS, mRNA and translations from feature tables
entret Retrieves sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
seqxref Retrieve all database cross-references for a sequence entry
seqxrefget Retrieve all cross-referenced data for a sequence entry
showalign Display a multiple sequence alignment in pretty format
whichdb Search all sequence databases for an entry and retrieve it

DATA RETRIEVAL TEXT DATA

Program name Description
drtext Get data resource entries complete text
entret Retrieves sequence entries from flatfile databases and files
ontotext Get ontology term(s) original full text
textget Get text data entries
textsearch Search the textual description of sequence(s)

DATA RETRIEVAL TOOL DATA

Program name Description
acdc Test an application ACD file
acdpretty Correctly reformat an application ACD file
acdtable Generate an HTML table of parameters from an application ACD file
acdtrace Trace processing of an application ACD file (for testing)
acdvalid Validate an application ACD file

DATA RETRIEVAL URL DATA

Program name Description
urlget Get URLs of data resources

DISPLAY

Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draws circular maps of DNA constructs
iep Calculate the isoelectric point of proteins
lindna Draws linear maps of DNA constructs
pepinfo Plot amino acid properties of a protein sequence in parallel
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
plotorf Plot potential open reading frames in a nucleotide sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showfeat Display features of a sequence in pretty format
showpep Displays protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs

DOCUMENTATION

Program name Description
seealso Finds programs with similar function to a specified program
tfm Displays full documentation for an application
wossdata Finds programs by EDAM data
wossinput Finds programs by EDAM input data
wossname Finds programs by keywords in their short description
wossoperation Finds programs by EDAM operation
wossoutput Finds programs by EDAM output data
wossparam Finds programs by EDAM parameter
wosstopic Finds programs by EDAM topic

EDIT

Program name Description
aligncopy Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Removes a section from a sequence
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieves sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
extractfeat Extract features from sequence(s)
extractseq Extract regions from a sequence
featcopy Reads and writes a feature table
featreport Reads and writes a feature table
feattext Return a feature table original text
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein sequences
maskambignuc Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks all ambiguity characters in protein sequences with X
maskfeat Write a sequence with masked features
maskseq Write a sequence with masked regions
newseq Create a sequence file from a typed-in sequence
nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn Remove carriage return from ASCII files
nospace Remove whitespace from an ASCII text file
notab Replace tabs with spaces in an ASCII text file
notseq Write to file a subset of an input stream of sequences
nthseq Write to file a single sequence from an input stream of sequences
nthseqset Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Reads and counts sequences
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of sequences
seqretsplit Reads sequences and writes them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) sequences, skipping first few
splitsource Split sequence(s) into original source sequences
splitter Split sequence(s) into smaller sequences
trimest Remove poly-A tails from nucleotide sequences
trimseq Remove unwanted characters from start and end of sequence(s)
trimspace Remove extra whitespace from an ASCII text file
union Concatenate multiple sequences into a single sequence
vectorstrip Removes vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file

ENZYME KINETICS

Program name Description
findkm Calculate and plot enzyme reaction data

FEATURE TABLES

Program name Description
extractfeat Extract features from sequence(s)
maskfeat Write a sequence with masked features
showfeat Display features of a sequence in pretty format
twofeat Finds neighbouring pairs of features in sequence(s)

NUCLEIC 2D STRUCTURE

Program name Description
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
einverted Finds inverted repeats in nucleotide sequences
sirna Finds siRNA duplexes in mRNA

NUCLEIC CODON USAGE

Program name Description
cai Calculate codon adaptation index
chips Calculates Nc codon usage statistic
codcmp Codon usage table comparison
codcopy Copy and reformat a codon usage table
cusp Create a codon usage table from nucleotide sequence(s)
syco Draw synonymous codon usage statistic plot for a nucleotide sequence

NUCLEIC COMPOSITION

Program name Description
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
chaos Draw a chaos game representation plot for a nucleotide sequence
compseq Calculate the composition of unique words in sequences
dan Calculates nucleic acid melting temperature
density Draw a nucleic acid density plot
freak Generate residue/base frequency table or plot
isochore Plots isochores in DNA sequences
wordcount Count and extract unique words in molecular sequence(s)

NUCLEIC CPG ISLANDS

Program name Description
cpgplot Identify and plot CpG islands in nucleotide sequence(s)
cpgreport Identify and report CpG-rich regions in nucleotide sequence(s)
geecee Calculate fractional GC content of nucleic acid sequences
newcpgreport Identify CpG islands in nucleotide sequence(s)
newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s)

NUCLEIC FUNCTIONAL SITES

Program name Description
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
sirna Finds siRNA duplexes in mRNA
trimest Remove poly-A tails from nucleotide sequences

NUCLEIC GENE FINDING

Program name Description
checktrans Reports STOP codons and ORF statistics of a protein
getorf Finds and extracts open reading frames (ORFs)
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
plotorf Plot potential open reading frames in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
syco Draw synonymous codon usage statistic plot for a nucleotide sequence
tcode Identify protein-coding regions using Fickett TESTCODE statistic
wobble Plot third base position variability in a nucleotide sequence

NUCLEIC MOTIFS

Program name Description
dreg Regular expression search of nucleotide sequence(s)
fuzznuc Search for patterns in nucleotide sequences
fuzztran Search for patterns in protein sequences (translated)

NUCLEIC MUTATION

Program name Description
msbar Mutate a sequence
shuffleseq Shuffles a set of sequences maintaining composition

NUCLEIC PRIMERS

Program name Description
eprimer3 Picks PCR primers and hybridization oligos
eprimer32 Picks PCR primers and hybridization oligos
primersearch Search DNA sequences for matches with primer pairs
stssearch Search a DNA database for matches with a set of STS primers

NUCLEIC PROFILES

Program name Description
profit Scan one or more sequences with a simple frequency matrix
prophecy Create frequency matrix or profile from a multiple alignment
prophet Scan one or more sequences with a Gribskov or Henikoff profile

NUCLEIC PROPERTIES

Program name Description
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
dan Calculates nucleic acid melting temperature

NUCLEIC REPEATS

Program name Description
einverted Finds inverted repeats in nucleotide sequences
equicktandem Finds tandem repeats in nucleotide sequences
etandem Finds tandem repeats in a nucleotide sequence
palindrome Finds inverted repeats in nucleotide sequence(s)

NUCLEIC RESTRICTION

Program name Description
recoder Find restriction sites to remove (mutate) with no translation change
redata Retrieve information from REBASE restriction enzyme database
remap Display restriction enzyme binding sites in a nucleotide sequence
restover Find restriction enzymes producing a specific overhang
restrict Report restriction enzyme cleavage sites in a nucleotide sequence
showseq Displays sequences with features in pretty format
silent Find restriction sites to insert (mutate) with no translation change

NUCLEIC TRANSCRIPTION

Program name Description
jaspscan Scans DNA sequences for transcription factors
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
tfscan Identify transcription factor binding sites in DNA sequences

NUCLEIC TRANSLATION

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
checktrans Reports STOP codons and ORF statistics of a protein
coderet Extract CDS, mRNA and translations from feature tables
plotorf Plot potential open reading frames in a nucleotide sequence
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
showseq Displays sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
transeq Translate nucleic acid sequences

ONTOLOGY

Program name Description
ontocount Count ontology term(s)
ontoget Get ontology term(s)
ontogetcommon Get common ancestor for terms
ontogetdown Get ontology term(s) by parent id
ontogetobsolete Get ontology ontology terms
ontogetroot Get ontology root terms by child identifier
ontogetsibs Get ontology term(s) by id with common parent
ontogetup Get ontology term(s) by id of child
ontoisobsolete Report whether an ontology term id is obsolete
ontotext Get ontology term(s) original full text

ONTOLOGY EDAM

Program name Description
drfinddata Find public databases by data type
drfindformat Find public databases by format
drfindid Find public databases by identifier
drfindresource Find public databases by resource
edamdef Find EDAM ontology terms by definition
edamhasinput Find EDAM ontology terms by has_input relation
edamhasoutput Find EDAM ontology terms by has_output relation
edamisformat Find EDAM ontology terms by is_format_of relation
edamisid Find EDAM ontology terms by is_identifier_of relation
edamname Find EDAM ontology terms by name
wossdata Finds programs by EDAM data
wossinput Finds programs by EDAM input data
wossoperation Finds programs by EDAM operation
wossoutput Finds programs by EDAM output data
wossparam Finds programs by EDAM parameter
wosstopic Finds programs by EDAM topic

ONTOLOGY GO

Program name Description
godef Find GO ontology terms by definition
goname Find GO ontology terms by name

ONTOLOGY TAXONOMY

Program name Description
taxget Get taxon(s)
taxgetdown Get descendants of taxon(s)
taxgetrank Get parents of taxon(s)
taxgetspecies Get all species under taxon(s)
taxgetup Get parents of taxon(s)

PHYLOGENY MOLECULAR SEQUENCE

Program name Description
distmat Create a distance matrix from a multiple sequence alignment

PROTEIN 2D STRUCTURE

Program name Description
garnier Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
pepcoil Predicts coiled coil regions in protein sequences
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence

PROTEIN 3D STRUCTURE

Program name Description
psiphi Calculates phi and psi torsion angles from protein coordinates

PROTEIN COMPOSITION

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
compseq Calculate the composition of unique words in sequences
emowse Search protein sequences by digest fragment molecular weight
freak Generate residue/base frequency table or plot
mwcontam Find weights common to multiple molecular weights files
mwfilter Filter noisy data from molecular weights file
oddcomp Identify proteins with specified sequence word composition
pepdigest Reports on protein proteolytic enzyme or reagent cleavage sites
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculates statistics of protein properties
wordcount Count and extract unique words in molecular sequence(s)

PROTEIN DOMAINS

Program name Description
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
pepcoil Predicts coiled coil regions in protein sequences

PROTEIN FUNCTIONAL SITES

Program name Description
sigcleave Reports on signal cleavage sites in a protein sequence
tmap Predict and plot transmembrane segments in protein sequences

PROTEIN MOTIFS

Program name Description
antigenic Finds antigenic sites in proteins
epestfind Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
patmatdb Searches protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
preg Regular expression search of protein sequence(s)
pscan Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave Reports on signal cleavage sites in a protein sequence

PROTEIN MUTATION

Program name Description
msbar Mutate a sequence
shuffleseq Shuffles a set of sequences maintaining composition

PROTEIN PROFILES

Program name Description
profit Scan one or more sequences with a simple frequency matrix
prophecy Create frequency matrix or profile from a multiple alignment
prophet Scan one or more sequences with a Gribskov or Henikoff profile

PROTEIN PROPERTIES

Program name Description
charge Draw a protein charge plot
hmoment Calculate and plot hydrophobic moment for protein sequence(s)
iep Calculate the isoelectric point of proteins
octanol Draw a White-Wimley protein hydropathy plot
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculates statistics of protein properties
pepwindow Draw a hydropathy plot for a protein sequence
pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment

UTILS

Program name Description
embossdata Find and retrieve EMBOSS data files
embossversion Reports the current EMBOSS version number

UTILS DATABASE CREATION

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
cutgextract Extract codon usage tables from CUTG database
jaspextract Extract data from JASPAR
printsextract Extract data from PRINTS database for use by pscan
prosextract Processes the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications
tfextract Process TRANSFAC transcription factor database for use by tfscan

UTILS DATABASE INDEXING

Program name Description
dbiblast Index a BLAST database
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
dbxcompress Compress an uncompressed dbx index
dbxedam Index the EDAM ontology using b+tree indices
dbxfasta Index a fasta file database using b+tree indices
dbxflat Index a flat file database using b+tree indices
dbxgcg Index a GCG formatted database using b+tree indices
dbxobo Index an obo ontology using b+tree indices
dbxreport Validate index and report internals for dbx databases
dbxresource Index a data resource catalogue using b+tree indices
dbxstat Dump statistics for dbx databases
dbxtax Index NCBI taxonomy using b+tree indices
dbxuncompress Uncompress a compressed dbx index