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 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
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
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
needleall 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
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