The Applications (programs)


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

Applications in the current release

Program name Description
aaindexextractExtract data from AAINDEX
abiviewReads ABI file and display the trace
acdcACD compiler
acdprettyACD pretty printing utility
acdtableCreates an HTML table from an ACD file
acdtraceACD compiler on-screen trace
acdvalidACD file validation
antigenicFinds antigenic sites in proteins
backtranseqBack translate a protein sequence
bananaBending and curvature plot in B-DNA
biosedReplace or delete sequence sections
btwistedCalculates the twisting in a B-DNA sequence
caiCAI codon adaptation index
chaosCreate a chaos game representation plot for a sequence
chargeProtein charge plot
checktransReports STOP codons and ORF statistics of a protein
chipsCodon usage statistics
cirdnaDraws circular maps of DNA constructs
codcmpCodon usage table comparison
coderetExtract CDS, mRNA and translations from feature tables
compseqCounts the composition of dimer/trimer/etc words in a sequence
consCreates a consensus from multiple alignments
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
cuspCreate a codon usage table
cutgextractExtract data from CUTG
cutseqRemoves a specified section from a sequence
danCalculates DNA RNA/DNA melting temperature
dbiblastIndex a BLAST database
dbifastaIndex a fasta database
dbiflatIndex a flat file database
dbigcgIndex a GCG formatted database
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
diffseqFind differences between nearly identical sequences
digestProtein proteolytic enzyme or reagent cleavage digest
distmatCreates a distance matrix from multiple alignments
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
dregRegular expression search of a nucleotide sequence
einvertedFinds DNA inverted repeats
embossdataFinds or fetches the data files read in by the EMBOSS programs
embossversionWrites the current EMBOSS version number
emmaMultiple alignment program - interface to ClustalW program
emowseProtein identification by mass spectrometry
entretReads and writes (returns) flatfile entries
epestfindFinds PEST motifs as potential proteolytic cleavage sites
eprimer3Picks PCR primers and hybridization oligos
equicktandemFinds tandem repeats
est2genomeAlign EST and genomic DNA sequences
etandemLooks for tandem repeats in a nucleotide sequence
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
findkmFind Km and Vmax for an enzyme reaction by a Hanes/Woolf plot
freakResidue/base frequency table or plot
fuzznucNucleic acid pattern search
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
garnierPredicts protein secondary structure
geeceeCalculates the fractional GC content of nucleic acid sequences
getorfFinds and extracts open reading frames (ORFs)
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
iepCalculates the isoelectric point of a protein
infoalignInformation on a multiple sequence alignment
infoseqDisplays some simple information about sequences
isochorePlots isochores in large DNA sequences
lindnaDraws linear maps of DNA constructs
listorWrites a list file of the logical OR of two sets of sequences
marscanFinds MAR/SAR sites in nucleic sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
matcherFinds the best local alignments between two sequences
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences
msbarMutate sequence beyond all recognition
mwcontamShows molwts that match across a set of files
mwfilterFilter noisy molwts from mass spec output
needleNeedleman-Wunsch global alignment
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
octanolDisplays protein hydropathy
oddcompFinds protein sequence regions with a biased composition
palindromeLooks for inverted repeats in a nucleotide sequence
pasteseqInsert one sequence into another
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pepinfoPlots simple amino acid properties in parallel
pepnetDisplays proteins as a helical net
pepstatsProtein statistics
pepwheelShows protein sequences as helices
pepwindowDisplays protein hydropathy
pepwindowallDisplays protein hydropathy of a set of sequences
plotconPlots the quality of conservation of a sequence alignment
plotorfPlot potential open reading frames
polydotDisplays all-against-all dotplots of a set of sequences
pregRegular expression search of a protein sequence
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
primersearchSearches DNA sequences for matches with primer pairs
printsextractExtract data from PRINTS
profitScan a sequence or database with a matrix or profile
prophecyCreates matrices/profiles from multiple alignments
prophetGapped alignment for profiles
prosextractBuilds the PROSITE motif database for patmatmotifs to search
pscanScans proteins using PRINTS
psiphiCalculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
rebaseextractExtract data from REBASE
recoderRemove restriction sites but maintain the same translation
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
revseqReverse and complement a sequence
seealsoFinds programs sharing group names
seqmatchallDoes an all-against-all comparison of a set of sequences
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showorfPretty output of DNA translations
showseqDisplay a sequence with features, translation etc
shuffleseqShuffles a set of sequences maintaining composition
sigcleaveReports protein signal cleavage sites
silentSilent mutation restriction enzyme scan
sirnaFinds siRNA duplexes in mRNA
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
stretcherFinds the best global alignment between two sequences
stssearchSearches a DNA database for matches with a set of STS primers
supermatcherFinds a match of a large sequence against one or more sequences
sycoSynonymous codon usage Gribskov statistic plot
tcodeFickett TESTCODE statistic to identify protein-coding DNA
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tfextractExtract data from TRANSFAC
tfmDisplays a program's help documentation manual
tfscanScans DNA sequences for transcription factors
tmapDisplays membrane spanning regions
tranalignAlign nucleic coding regions given the aligned proteins
transeqTranslate nucleic acid sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
twofeatFinds neighbouring pairs of features in sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
waterSmith-Waterman local alignment
whichdbSearch all databases for an entry
wobbleWobble base plot
wordcountCounts words of a specified size in a DNA sequence
wordmatchFinds all exact matches of a given size between 2 sequences
wossnameFinds programs by keywords in their one-line documentation
yankReads a sequence range, appends the full USA to a list file