| 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 | Reads and writes alignments
aligncopypair | Reads and writes pairs from alignments
antigenic | Finds antigenic sites in proteins
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
cai | Calculate codon adaptation index
chaos | Draw a chaos game representation plot for a nucleotide sequence
charge | Draw a protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein
chips | Calculates Nc codon usage statistic
cirdna | Draws circular maps 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 | Removes a section from a sequence
dan | Calculates 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
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
degapseq | Removes 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
digest | Reports on protein proteolytic enzyme or reagent cleavage sites
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 | Displays a wordmatch dotplot of two sequences
dreg | Regular expression search of nucleotide sequence(s)
edialign | Local multiple alignment of sequences
einverted | Finds inverted repeats in nucleotide sequences
embossdata | Find and retrieve EMBOSS data files
embossversion | Reports the current EMBOSS version number
emma | Multiple sequence alignment (ClustalW wrapper)
emowse | Search protein sequences by digest fragment molecular weight
entret | Retrieves sequence entries from flatfile databases and files
epestfind | Finds PEST motifs as potential proteolytic cleavage sites
eprimer3 | Picks PCR primers and hybridization oligos
equicktandem | Finds tandem repeats in nucleotide sequences
est2genome | Align EST sequences to genomic DNA sequence
etandem | Finds 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 | Reads and writes a feature table
featreport | Reads and writes a feature table
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 | Predicts protein secondary structure using GOR method
geecee | Calculate fractional GC content of nucleic acid sequences
getorf | Finds and extracts open reading frames (ORFs)
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
infobase | Return information on a given nucleotide base
inforesidue | Return information on a given amino acid residue
infoseq | Display basic information about sequences
isochore | Plots isochores in DNA sequences
jaspextract | Extract data from JASPAR
jaspscan | Scans DNA sequences for transcription factors
lindna | Draws 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 | Finds matrix/scaffold recognition (MRS) signatures in DNA 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
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 all 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
octanol | Draw a White-Wimley protein hydropathy plot
oddcomp | Identify proteins with specified sequence word composition
palindrome | Finds inverted repeats in nucleotide sequence(s)
pasteseq | Insert one sequence into another
patmatdb | Searches protein sequences with a sequence motif
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database
pepcoil | Predicts coiled coil regions in protein sequences
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepnet | Draw a helical net for a protein sequence
pepstats | Calculates 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 | Processes the PROSITE motif database for use by patmatmotifs
pscan | Scans 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
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 | Finds programs with similar function to a specified program
seqmatchall | All-against-all word comparison of a sequence set
seqret | Reads and writes (returns) sequences
seqretsetall | Reads and writes (returns) many sets of sequences
seqretsplit | Reads sequences and writes them to individual files
showalign | Display a multiple sequence alignment in pretty format
showdb | Displays information on configured databases
showfeat | Display features of a sequence in pretty format
showorf | Display a nucleotide sequence and translation in pretty format
showpep | Displays protein sequences with features in pretty format
showseq | Displays sequences with features in pretty format
shuffleseq | Shuffles a set of sequences maintaining composition
sigcleave | Reports on signal cleavage sites in a protein sequence
silent | Find restriction sites to insert (mutate) with no translation change
sirna | Finds 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 | Reads and writes (returns) 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
tcode | Identify protein-coding regions using Fickett TESTCODE statistic
textsearch | Search the textual description of sequence(s)
tfextract | Process TRANSFAC transcription factor database for use by tfscan
tfm | Displays 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 | Finds neighbouring pairs of features in sequence(s)
union | Concatenate multiple sequences into a single sequence
vectorstrip | Removes 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 | Finds regions of identity (exact matches) of two sequences
wossname | Finds programs by keywords in their short description
yank | Add a sequence reference (a full USA) to a list file