| The Applications (programs)

The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

### Applications in the current release

Program name | Description
--- | ---
aaindexextract | Extract amino acid property data from AAINDEX
abiview | Display the trace in an ABI sequencer file
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
aligncopy | Read and write alignments
aligncopypair | Read and write pairs from alignments
antigenic | Find antigenic sites in proteins
assemblyget | Get assembly of sequence reads
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
banana | Plot bending and curvature data for B-DNA
biosed | Replace or delete sequence sections
btwisted | Calculate the twisting in a B-DNA sequence
cachedas | Generate server cache file for DAS servers or for the DAS registry
cachedbfetch | Generate server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch | Generate server cache file for EB-eye search domains
cacheensembl | Generate server cache file for an Ensembl server
cai | Calculate codon adaptation index
chaos | Draw a chaos game representation plot for a nucleotide sequence
charge | Draw a protein charge plot
checktrans | Report STOP codons and ORF statistics of a protein
chips | Calculate Nc codon usage statistic
cirdna | Draw circular map of DNA constructs
codcmp | Codon usage table comparison
codcopy | Copy and reformat a codon usage table
coderet | Extract CDS, mRNA and translations from feature tables
compseq | Calculate the composition of unique words in sequences
cons | Create a consensus sequence from a multiple alignment
consambig | Create an ambiguous consensus sequence from a multiple alignment
cpgplot | Identify and plot CpG islands in nucleotide sequence(s)
cpgreport | Identify and report CpG-rich regions in nucleotide sequence(s)
cusp | Create a codon usage table from nucleotide sequence(s)
cutgextract | Extract codon usage tables from CUTG database
cutseq | Remove a section from a sequence
dan | Calculate nucleic acid melting temperature
dbiblast | Index a BLAST database
dbifasta | Index a fasta file database
dbiflat | Index a flat file database
dbigcg | Index a GCG formatted database
dbtell | Display information about a public 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
degapseq | Remove non-alphabetic (e.g. gap) characters from sequences
density | Draw a nucleic acid density plot
descseq | Alter the name or description of a sequence
diffseq | Compare and report features of two similar sequences
distmat | Create a distance matrix from a multiple sequence alignment
dotmatcher | Draw a threshold dotplot of two sequences
dotpath | Draw a non-overlapping wordmatch dotplot of two sequences
dottup | Display a wordmatch dotplot of two sequences
dreg | Regular expression search of nucleotide sequence(s)
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
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
edialign | Local multiple alignment of sequences
einverted | Find inverted repeats in nucleotide sequences
embossdata | Find and retrieve EMBOSS data files
embossupdate | Checks for more recent updates to EMBOSS
embossversion | Report the current EMBOSS version number
emma | Multiple sequence alignment (ClustalW wrapper)
emowse | Search protein sequences by digest fragment molecular weight
entret | Retrieve sequence entries from flatfile databases and files
epestfind | Find PEST motifs as potential proteolytic cleavage sites
eprimer3 | Pick PCR primers and hybridization oligos
eprimer32 | Pick PCR primers and hybridization oligos
equicktandem | Find tandem repeats in nucleotide sequences
est2genome | Align EST sequences to genomic DNA sequence
etandem | Find tandem repeats in a nucleotide sequence
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from sequence(s)
extractseq | Extract regions from a sequence
featcopy | Read and write a feature table
featmerge | Merge two overlapping feature tables
featreport | Read and write a feature table
feattext | Return a feature table original text
findkm | Calculate and plot enzyme reaction data
freak | Generate residue/base frequency table or plot
fuzznuc | Search for patterns in nucleotide sequences
fuzzpro | Search for patterns in protein sequences
fuzztran | Search for patterns in protein sequences (translated)
garnier | Predict protein secondary structure using GOR method
geecee | Calculate fractional GC content of nucleic acid sequences
getorf | Find and extract open reading frames (ORFs)
godef | Find GO ontology terms by definition
goname | Find GO ontology terms by name
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
hmoment | Calculate and plot hydrophobic moment for protein sequence(s)
iep | Calculate the isoelectric point of proteins
infoalign | Display basic information about a multiple sequence alignment
infoassembly | Display information about assemblies
infobase | Return information on a given nucleotide base
inforesidue | Return information on a given amino acid residue
infoseq | Display basic information about sequences
isochore | Plot isochores in DNA sequences
jaspextract | Extract data from JASPAR
jaspscan | Scan DNA sequences for transcription factors
lindna | Draw linear maps of DNA constructs
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Create random nucleotide sequences
makeprotseq | Create random protein sequences
marscan | Find matrix/scaffold recognition (MRS) signatures in DNA sequences
maskambignuc | Mask all ambiguity characters in nucleotide sequences with N
maskambigprot | Mask all ambiguity characters in protein sequences with X
maskfeat | Write a sequence with masked features
maskseq | Write a sequence with masked regions
matcher | Waterman-Eggert local alignment of two sequences
megamerger | Merge two large overlapping DNA sequences
merger | Merge two overlapping sequences
msbar | Mutate a sequence
mwcontam | Find weights common to multiple molecular weights files
mwfilter | Filter noisy data from molecular weights file
needle | Needleman-Wunsch global alignment of two sequences
needleall | Many-to-many pairwise alignments of two sequence sets
newcpgreport | Identify CpG islands in nucleotide sequence(s)
newcpgseek | Identify and report CpG-rich regions in nucleotide sequence(s)
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 | Read and write (return) one set of sequences from many
octanol | Draw a White-Wimley protein hydropathy plot
oddcomp | Identify proteins with specified sequence word composition
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
palindrome | Find inverted repeats in nucleotide sequence(s)
pasteseq | Insert one sequence into another
patmatdb | Search protein sequences with a sequence motif
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database
pepcoil | Predict coiled coil regions in protein sequences
pepdigest | Report on protein proteolytic enzyme or reagent cleavage sites
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepnet | Draw a helical net for a protein sequence
pepstats | Calculate statistics of protein properties
pepwheel | Draw a helical wheel diagram for a protein sequence
pepwindow | Draw a hydropathy plot for a protein sequence
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
plotcon | Plot conservation of a sequence alignment
plotorf | Plot potential open reading frames in a nucleotide sequence
polydot | Draw dotplots for all-against-all comparison of a sequence set
preg | Regular expression search of protein sequence(s)
prettyplot | Draw a sequence alignment with pretty formatting
prettyseq | Write a nucleotide sequence and its translation to file
primersearch | Search DNA sequences for matches with primer pairs
printsextract | Extract data from PRINTS database for use by pscan
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
prosextract | Process the PROSITE motif database for use by patmatmotifs
pscan | Scan protein sequence(s) with fingerprints from the PRINTS database
psiphi | Calculates phi and psi torsion angles from protein coordinates
rebaseextract | Process the REBASE database for use by restriction enzyme applications
recoder | Find restriction sites to remove (mutate) with no translation change
redata | Retrieve information from REBASE restriction enzyme database
refseqget | Get reference sequence
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
revseq | Reverse and complement a nucleotide sequence
seealso | Find programs with similar function to a specified program
seqcount | Read and count sequences
seqmatchall | All-against-all word comparison of a sequence set
seqret | Read and write (return) sequences
seqretsetall | Read and write (return) many sets of sequences
seqretsplit | Read sequences and write them to individual files
seqxref | Retrieve all database cross-references for a sequence entry
seqxrefget | Retrieve all cross-referenced data for a sequence entry
servertell | Display information about a public server
showalign | Display a multiple sequence alignment in pretty format
showdb | Display information on configured databases
showfeat | Display features of a sequence in pretty format
showorf | Display a nucleotide sequence and translation in pretty format
showpep | Display protein sequences with features in pretty format
showseq | Display sequences with features in pretty format
showserver | Display information on configured servers
shuffleseq | Shuffle a set of sequences maintaining composition
sigcleave | Report on signal cleavage sites in a protein sequence
silent | Find restriction sites to insert (mutate) with no translation change
sirna | Find siRNA duplexes in mRNA
sixpack | Display a DNA sequence with 6-frame translation and ORFs
sizeseq | Sort sequences by size
skipredundant | Remove redundant sequences from an input set
skipseq | Read and write (return) sequences, skipping first few
splitsource | Split sequence(s) into original source sequences
splitter | Split sequence(s) into smaller sequences
stretcher | Needleman-Wunsch rapid global alignment of two sequences
stssearch | Search a DNA database for matches with a set of STS primers
supermatcher | Calculate approximate local pair-wise alignments of larger sequences
syco | Draw synonymous codon usage statistic plot for a nucleotide sequence
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)
tcode | Identify protein-coding regions using Fickett TESTCODE statistic
textget | Get text data entries
textsearch | Search the textual description of sequence(s)
tfextract | Process TRANSFAC transcription factor database for use by tfscan
tfm | Display full documentation for an application
tfscan | Identify transcription factor binding sites in DNA sequences
tmap | Predict and plot transmembrane segments in protein sequences
tranalign | Generate an alignment of nucleic coding regions from aligned proteins
transeq | Translate nucleic acid 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
twofeat | Find neighbouring pairs of features in sequence(s)
union | Concatenate multiple sequences into a single sequence
urlget | Get URLs of data resources
variationget | Get sequence variations
vectorstrip | Remove vectors from the ends of nucleotide sequence(s)
water | Smith-Waterman local alignment of sequences
whichdb | Search all sequence databases for an entry and retrieve it
wobble | Plot third base position variability in a nucleotide sequence
wordcount | Count and extract unique words in molecular sequence(s)
wordfinder | Match large sequences against one or more other sequences
wordmatch | Find regions of identity (exact matches) of two sequences
wossdata | Find programs by EDAM data
wossinput | Find programs by EDAM input data
wossname | Find programs by keywords in their short description
wossoperation | Find programs by EDAM operation
wossoutput | Find programs by EDAM output data
wossparam | Find programs by EDAM parameter
wosstopic | Find programs by EDAM topic
yank | Add a sequence reference (a full USA) to a list file