The Applications (programs)

Contents

• Introduction
• Groups of applications
• List of applications
• EMBASSY programs
• Proposed new applications

Introduction

Applications in the current release

Program name	Author(s)	Description
aaindexextract	RFCGR	Extract data from AAINDEX
abiview	RFCGR	Reads ABI file and display the trace
acdc	Sanger	Tests definition files for any EMBOSS application.
antigenic	RFCGR	Finds antigenic sites in proteins
backtranseq	RFCGR	Back translate a protein sequence
banana	Sanger	Bending and Curvature Plot in B-DNA
biosed	RFCGR	Replace or delete sequence sections
btwisted	RFCGR	Calculates the twisting in a B-DNA sequence
cai	RFCGR	CAI codon usage statistic
chaos	Sanger	Create a chaos plot for a sequence.
charge	RFCGR	Protein charge plot
checktrans	EBI	ORF property statistics
chips	RFCGR	Codon usage statistics
cirdna	Norway	Draws circular maps of DNA constructs
codcmp	RFCGR	Codon usage table comparison
coderet	RFCGR	Extract CDS, mRNA and translations from feature tables
compseq	RFCGR	Counts the composition of dimer/trimer/etc words in a sequence
cons	RFCGR	Creates a consensus from multiple alignments
cpgplot	RFCGR	Plot CpG rich areas
cpgreport	RFCGR	Reports CpG rich regions
cusp	RFCGR	Create a codon usage table
cutgextract	HGMP	Extract data from CUTG
cutseq	RFCGR	Removes a specified section from a sequence.
dan	RFCGR	Plot melting temperatures for DNA.
dbiblast	Sanger	Database indexing for BLAST 1 and 2 indexed databases
dbifasta	RFCGR	Index a fasta database
dbiflat	Sanger	Database indexing for flat file databases
dbigcg	Sanger	Database indexing for GCG formatted databases
dbxfasta	RFCGR	Database b+tree indexing for fasta file databases
dbxflat	RFCGR	Database b+tree indexing for flat file databases
dbxgcg	RFCGR	Database b+tree indexing for GCG formatted databases
degapseq	RFCGR	Removes gap characters from sequences
descseq	RFCGR	Alter the name or description of a sequence.
diffseq	RFCGR	Find differences between nearly identical sequences
digest	RFCGR	Protein proteolytic enzyme or reagent cleavage digest
distmat	RFCGR	Creates a distance matrix from multiple alignments
dotmatcher	Sanger	Produces a dotplot of two sequences.
dotpath	RFCGR	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Sanger	DNA sequence dot plot
dreg	Sanger	Regular expression search of a nucleotide sequence
einverted	Sanger	Finds DNA inverted repeats
embossdata	RFCGR	Finds or fetches the data files read in by the EMBOSS programs
embossversion	RFCGR	Writes the current EMBOSS version number
emowse	RFCGR	Protein identification by mass spectrometry
emma	RFCGR	Multiple alignment program
entret	RFCGR	Reads and writes (returns) flatfile entries
epestfind	Austria	Finds PEST motifs as potential proteolytic cleavage sites
eprimer3	RFCGR	Picks PCR primers and hybridization oligos
equicktandem	Sanger	Finds tandem repeats
est2genome	Sanger	Align EST and genomic DNA sequences
etandem	Sanger	Looks for tandem repeats in a nucleotide sequence.
extractfeat	RFCGR	Extract features from a sequence
extractseq	RFCGR	Extract regions from a sequence.
findkm	RFCGR	Calculates Km and Vmax for an enzyme reaction
freak	RFCGR	Residue/base frequency table or plot
fuzznuc	RFCGR	Nucleic acid pattern search
fuzzpro	RFCGR	Protein pattern search
fuzztran	RFCGR	Protein pattern search after translation
garnier	EBI	Predicts protein secondary structure
geecee	Sanger	Calculates the fractional GC content of nucleic acid sequences
getorf	RFCGR	Finds and extracts open reading frames (ORFs)
helixturnhelix	RFCGR	Finds nucleic acid binding domains.
hmoment	RFCGR	Hydrophobic moment calculation
iep	RFCGR	Calculates the isoelectric point of a protein
infoalign	RFCGR	Information on a multiple sequence alignment
infoseq	RFCGR	Displays some simple information about sequences
isochore	Sanger	Plots isochores in large DNA sequences
jembossctl	RFCGR	Jemboss Authentication Control
lindna	Norway	Draws linear maps of DNA constructs
listor	RFCGR	Writes a list file of the logical OR of two sets of sequences
marscan	RFCGR	Finds MAR/SAR sites in nucleic sequences
maskfeat	RFCGR	Mask off features of a sequence
maskseq	RFCGR	Mask off regions of a sequence.
matcher	Sanger	Local alignment of two sequences
megamerger	RFCGR	Merge two large overlapping nucleic acid sequences
merger	RFCGR	Merge two overlapping sequences
msbar	RFCGR	Mutate sequence beyond all recognition
mwcontam	RFCGR	Shows molwts that match across a set of files
mwfilter	RFCGR	Filter noisy molwts from mass spec output
needle	RFCGR	Needleman-Wunsch global alignment.
newcpgreport	EBI	Report CpG rich areas
newcpgseek	EBI	Reports CpG rich regions
newseq	RFCGR	Type in a short new sequence.
noreturn	RFCGR	Removes carriage return from ASCII files
notseq	RFCGR	Excludes a set of sequences and writes out the remaining ones
nthseq	RFCGR	Writes one sequence from a multiple set of sequences
octanol	Sanger	Displays protein hydropathy
oddcomp	Norway	Finds protein sequence regions with a biased composition.
palindrome	RFCGR	Looks for inverted repeats in a nucleotide sequence.
pasteseq	RFCGR	Insert one sequence into another.
patmatdb	RFCGR	Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs	RFCGR	Compares a protein sequence to the PROSITE motif database.
pepcoil	RFCGR	Predicts coiled coil regions
pepinfo	RFCGR	Plots simple amino acid properties in parallel
pepnet	RFCGR	Protein helical net plot
pepstats	RFCGR	Protein statistics
pepwheel	RFCGR	Shows protein sequences as helices
pepwindow	Sanger	Displays protein hydropathy
pepwindowall	Sanger	Displays protein hydropathy of a set of sequences
plotcon	RFCGR	Plots the quality of conservation of a sequence alignment
plotorf	RFCGR	Plot potential open reading frames
polydot	Sanger	Multiple dotplot
preg	Sanger	Regular expression search of a protein sequence
prettyplot	Sanger	Displays aligned sequences, with colouring and boxing.
prettyseq	RFCGR	Output sequence with translated ranges
primersearch	RFCGR	Searches DNA sequences for matches with primer pairs
printsextract	RFCGR	Preprocesses the PRINTS database for use with the program PSCAN
profit	RFCGR	Scan a sequence or database with a matrix or profile
prophecy	RFCGR	Creates matrices/profiles from multiple alignments
prophet	RFCGR	Gapped alignment for profiles
prosextract	RFCGR	Extracts ID, AC, and PA lines from the PROSITE motif database.
pscan	RFCGR	Locates fingerprints (multiple motif features) in a protein sequence.
psiphi	RFCGR	Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
rebaseextract	RFCGR	Extract data from REBASE
recoder	RFCGR	Find and remove restriction sites but maintain the same translation
redata	RFCGR	Isoschizomers, references and Suppliers for Restriction Enzymes
remap	RFCGR	Display a sequence with restriction cut sites, translation etc..
restover	Sloan-Kettering Cancer Center	Finds restriction enzymes that produce a specific overhang
restrict	RFCGR	Finds Restriction Enzyme Cleavage Sites
revseq	RFCGR	Reverse and complement a sequence.
seealso	RFCGR	Finds programs sharing group names
seqmatchall	Sanger	Does an all-against-all comparison of a set of sequences
seqret	Sanger	Reads and writes (returns) a sequence.
seqretsplit	RFCGR	Reads and writes (returns) sequences in individual files
showdb	RFCGR	Displays information on the currently available databases
showalign	RFCGR	Display a multiple sequence alignment
showfeat	RFCGR	Show features of a sequence.
showorf	RFCGR	Pretty output of DNA translations
showseq	RFCGR	Display a sequence with features, translation etc
shuffleseq	RFCGR	Shuffles a set of sequences maintaining composition
sigcleave	RFCGR	Predicts signal peptide cleavage sites
silent	RFCGR	Silent mutation restriction enzyme scan
sirna	RFCGR	Finds siRNA duplexes in mRNA
sixpack	LION	Display a DNA sequence with 6-frame translation and ORFs
skipseq	RFCGR	Reads and writes (returns) sequences, skipping the first few
splitter	RFCGR	Split a sequence into (overlapping) smaller sequences.
stretcher	Sanger	Global alignment of two sequences.
stssearch	Sanger	Searches a DNA database for matches with a set of STS primers
supermatcher	Sanger	Finds a match of a large sequence against one or more sequences
syco	RFCGR	Synonymous codon usage Gribskov statistic plot
tcode	RFCGR	Fickett TESTCODE statistic to identify protein-coding DNA
textsearch	RFCGR	Search sequence documentation text. SRS and Entrez are faster!
tfextract	RFCGR	Extract data from TRANSFAC
tfm	RFCGR	Displays a program's help documentation manual
tfscan	RFCGR	Scans DNA sequences for transcription factors.
tmap	Sanger	Predict transmembrane proteins
tranalign	RFCGR	Align nucleic coding regions given the aligned proteins
transeq	RFCGR	Translates nucleic acid sequences.
trimest	RFCGR	Trim poly-A tails off EST sequences
trimseq	RFCGR	Trim ambiguous bits off the ends of sequences
twofeat	RFCGR	Finds neighbouring pairs of features in sequences
union	LION	Reads sequence fragments and builds one sequence
vectorstrip	RFCGR	Strips out DNA between a pair of vector sequences
water	RFCGR	Smith-Waterman local alignment.
whichdb	RFCGR	Search all databases for an entry
wobble	RFCGR	Wobble base plot
wordcount	Sanger	Counts words of a specified size in a DNA sequence.
wordmatch	Sanger	Finds all exact matches of a given size between 2 sequences
wossname	RFCGR	Finds programs by keywords in their one-line documentation.
yank	LION	Reads a range from a sequence, appends the full USA to a list file

EMBASSY

This allows the EMBOSS libraries to link to other software, and only requires that software to have an LGPL-compatible licence. Phylip, for example, fits this model.

But, to the user they do look exactly like EMBOSS aplications.

EMBASSY - PHYLIP

PHYLIP 3.61 has being converted as PHYLIPNEW and was released with EMBOSS 3.0.0 as a beta version.

The first release was named PHYLIP. We have not yet decided on the final name. See below for more details.

EMBASSY - PHYLIPNEW

The PHYLIPNEW versions of these programs all have the prefix "f" to distinguish them from the original programs. Although we take care to check that the EMBOSS versions will give the same results as the original programs, we recommend that if the results are used for publication you should check that you get the same results with both for your specific inputs.

Program name	Author(s)	Description
fclique	Joe Felsenstein	Largest clique program
fconsense	Joe Felsenstein	Majority-rule and strict consensus tree
fcontml	Joe Felsenstein	Continuous character Maximum Likelihood method
fcontrast	Joe Felsenstein	Continuous character Contrasts
fdiscboot	Joe Felsenstein	Bootstrapped discrete sites algorithm
fdnacomp	Joe Felsenstein	DNA compatibility algorithm
fdnadist	Joe Felsenstein	Nucleic acid sequence Distance Matrix program
fdnainvar	Joe Felsenstein	Nucleic acid sequence Invariants method
fdnaml	Joe Felsenstein	Estimates phylogenies from nucleic acid sequence Maximum Likelihood
fdnamlk	Joe Felsenstein	Estimates phylogenies from nucleic acid sequence Maximum Likelihood with molecular clock
fdnamove	Joe Felsenstein	Interactive DNA parsimony
fdnapars	Joe Felsenstein	DNA parsimony algorithm
fdnapenny	Joe Felsenstein	Penny algorithm for DNA
fdollop	Joe Felsenstein	Dollo and polymorphism parsimony algorithm
fdolmove	Joe Felsenstein	Interactive Dollo and Polymorphism Parsimony
fdolpenny	Joe Felsenstein	Penny algorithm Dollo or polymorphism
fdrawgram	Joe Felsenstein	Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree	Joe Felsenstein	Plots an unrooted tree diagram
ffactor	Joe Felsenstein	Multistate to binary recoding program
ffitch	Joe Felsenstein	Fitch-Margoliash and Least-Squares Distance Methods
ffreqboot	Joe Felsenstein	Bootstrapped sequences algorithm
fgendist	Joe Felsenstein	Compute genetic distances from gene frequencies
fkitsch	Joe Felsenstein	Fitch-Margoliash method with contemporary tips
fmix	Joe Felsenstein	Mixed parsimony algorithm
fmove	Joe Felsenstein	Interactive mixed method parsimony
fneighbor	Joe Felsenstein	Phylogenies from distance matrix by N-J or UPGMA method
fpars	Joe Felsenstein	Discrete character parsimony
fpenny	Joe Felsenstein	Penny algorithm, branch-and-bound to find all most parsimonious trees
fproml	Joe Felsenstein	Protein maximum Likelihood program
fpromlk	Joe Felsenstein	Protein maximum Likelihood program with molecular clock
fprotdist	Joe Felsenstein	Protein distance algorithm
fprotpars	Joe Felsenstein	Protein parsimony algorithm
frestboot	Joe Felsenstein	Bootstrapped sequences algorithm
frestdist	Joe Felsenstein	compute distance matrix from restriction sites or fragments
frestml	Joe Felsenstein	Restriction site maximum Likelihood method
fretree	Joe Felsenstein	Interactive tree rearrangement
fseqboot	Joe Felsenstein	Bootstrapped sequences algorithm
fseqbootall	Joe Felsenstein	Bootstrapped sequences algorithm
ftreedist	Joe Felsenstein	Distances between trees
ftreedistpair	Joe Felsenstein	Distances between trees

EMBASSY - DOMAINATRIX

Program name	Author(s)	Description
scopparse	RFCGR	Reads raw SCOP classification files and writes a DCF file.
cathparse	RFCGR	Reads raw CATH classification files and writes a DCF file.
domainreso	RFCGR	Removes low resolution domains from a DCF file.
domainseqs	RFCGR	Adds sequence records to a DCF file.
domainnr	RFCGR	Removes redundant domains from a DCF file. The file must contain domain sequence information which can be added by using DOMAINSEQS.
domainsse	RFCGR	Adds secondary structure records to a DCF file.
ssematch	RFCGR	Searches a DCF file for secondary structure matches. The file must contain domain secondary structure information which can be added by using DOMAINSEQS.

EMBASSY - DOMALIGN

Program name	Author(s)	Description
domainrep	RFCGR	Reorder DCF file so that the representative structure of each user-specified node is given first.
domainalign	RFCGR	Generates structure-based sequence alignments for nodes in a DCF file.
seqalign	RFCGR	Reads a DAF file and a DHF and writes a DAF file extended with the hits.
allversusall	RFCGR	Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values.

EMBASSY - DOMSEARCH

Program name	Author(s)	Description
seqsearch	RFCGR	Generate DHF files of database hits (sequences) from a DAF file (or other file of sequences) by using PSI-BLAST.
seqfraggle	RFCGR	Removes fragments from DHF files (or other files of sequences).
seqsort	RFCGR	Reads DHF files of database hits (sequences) and removes hits of ambiguous classification.
seqnr	RFCGR	Removes redundancy from DHF files (or other files of sequences).
seqwords	RFCGR	Generates DHF files of database hits (sequences) from Swissprot matching keywords from a keywords file.

EMBASSY - SIGNATURE

Program name	Author(s)	Description
siggen	RFCGR	Generates a sparse protein signature from an alignment and residue contact data.
sigscan	RFCGR	Generates a DHF of hits (sequences) from scanning a signature against a sequence database.
libgen	RFCGR	Generates various type of discriminator for each alignment in a directory.
libscan	RFCGR	Generates hits (sequences in a domain hits file) from searches of various types of discriminator (HMMs, profiles etc) against a sequence database. Or generates hits from screening sequences against a library of such discriminators.
rocon	RFCGR	Reads a DHF file of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a "hits file" for the hits, which are classified and rank-ordered on the basis of score.
rocplot	RFCGR	A generic and flexible tool for interpretation and graphical display of the performance of predictive methods using receiver Operator Characteristic (ROC) analysis.
matgen3d	RFCGR	Generates a 3D-1D scoring matrix from CCF files (clean coordinate files).
siggenlig	RFCGR	Generates ligand-binding signatures from a CON file (contacts file) of residue-ligand contacts.
sigscanlig	RFCGR	Generates a LHF (ligand hits file) of hits (sequences) from scanning a sequence against a library of ligand-binding signatures

EMBASSY - STRUCTURE

Program name	Author(s)	Description
pdbparse	RFCGR	Parses PDB files and writes CCF files for proteins.
pdbplus	RFCGR	Add records for residue solvent accessibility and secondary structure to a CCF file.
domainer	RFCGR	Reads CCF files for proteins and writes CCF files for domains in a DCF file.
contacts	RFCGR	Reads CCF files and writes CON files of intra-chain residue-residue contact data.
interface	RFCGR	Reads protein CCF files and writes CON files of inter-chain residue-residue contact data.
sites	RFCGR	Reads CCF files and writes CON files of residue-ligand contact data for domains in a DCF file.
hetparse	RFCGR	Converts raw dictionary of heterogen groups to EMBL-like format.
pdbtosp	RFCGR	Convert raw swissprot:PDB equivalence file to EMBL-like format.

EMBASSY - RECONSTRUCT

Program name	Author(s)	Description
alignrunner	Damian Counsell, RFCGR	Runs alignment program on all sequence pairs in a directory
comparator	Damian Counsell, RFCGR	Compare contact scores of two sequence alignments
contactalign	Damian Counsell, RFCGR	EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm
contactcount	Damian Counsell, RFCGR	Count specific versus non-specific contacts
degapseqrunner	Damian Counsell, RFCGR	Runs degapseq program on all sequence pairs in a directory
nawalign	Damian Counsell, RFCGR	Damian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm
nawalignrunner	Damian Counsell, RFCGR	Runs nawalign alignment program on all sequence pairs in a directory
needlerunner	Damian Counsell, RFCGR	Runs needle alignment program on all sequence pairs in a directory
scorecmapdir	Damian Counsell, RFCGR	Contact scores for cleaned protein chain contact files
scorer	Damian Counsell, RFCGR	Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment
scorerrunner	Damian Counsell, RFCGR	Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third
substitute	Damian Counsell, RFCGR	Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence)
substituterunner	Damian Counsell, RFCGR	Runs substitute on directory of traces and writes substituted sequences to another

EMBASSY - HMMER

The HMMER versions of these programs all have the prefix "e" to distinguish them from the original programs. Although we take care to check that the EMBOSS versions will give the same results as the original programs, we recommend that if the results are used for publication you should check that you get the same results with both for your specific inputs.

Program name	Author(s)	Description
ealistat	Sean Eddy	Statistics for multiple alignment files
ehmmalign	Sean Eddy	Align sequences with an HMM
ehmmbuild	Sean Eddy	Build HMM
ehmmcalibrate	Sean Eddy	Calibrate a hidden Markov model
ehmmconvert	Sean Eddy	Convert between HMM formats
ehmmemit	Sean Eddy	Extract HMM sequences
ehmmfetch	Sean Eddy	Extract HMM from a database
ehmmindex	Sean Eddy	Index an HMM database
ehmmpfam	Sean Eddy	Align single sequence with an HMM
ehmmsearch	Sean Eddy	Search sequence database with an HMM

EMBASSY - OTHERS