| 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
--- | ---
aaindexextract | Extract data from AAINDEX
abiview | Reads ABI file and display the trace
antigenic | Finds antigenic sites in proteins
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
coderet | Extract CDS, mRNA and translations from feature tables
compseq | Counts the 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 | Index a fasta database
dbiflat | Index a flat file database
dbigcg | Index a GCG formatted database
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 | Displays a 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 the data files read in by the 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
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 by a Hanes/Woolf plot
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 the 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 | Writes a list file of the logical OR of two sets of 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 nucleic acid 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 | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
octanol | Displays protein hydropathy
oddcomp | Finds 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
pestfind | Finds PEST motifs as potential proteolytic cleavage sites
plotcon | Plots the 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 | Builds the PROSITE motif database for patmatmotifs to search
pscan | Scans proteins using PRINTS
rebaseextract | Extract data from REBASE
recoder | Remove restriction sites but maintain the same translation
redata | Search REBASE for enzyme name, references, suppliers etc
remap | Display a sequence with restriction cut sites, translation etc
restover | Finds restriction enzymes that produce a specific overhang
restrict | Finds restriction enzyme cleavage sites
revseq | Reverse and complement a sequence
seealso | Finds programs sharing group names
seqmatchall | Does an 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 the first few
splitter | Split a sequence into (overlapping) smaller sequences
stretcher | Finds the best global alignment between two sequences
stssearch | Searches a DNA database for matches with a set of STS primers
supermatcher | Finds a match of a large sequence against one or more sequences
syco | Synonymous codon usage Gribskov statistic plot
tcode | Fickett TESTCODE statistic to identify protein-coding DNA
textsearch | Search sequence documentation text. SRS and Entrez are faster!
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