The Applications (programs)

Contents

• Applications by name
• Applications by group
• EMBASSY programs

Applications by name

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
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.
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

Applications by group

Applications by name

Group	Description
Alignment consensus	Alignment consensus
Alignment differences	Alignment differences
Alignment dot plots	Alignment dot plots
Alignment global	Alignment global
Alignment local	Alignment local
Alignment multiple	Alignment multiple
Display	Display
Edit	Edit
Enzyme kinetics	Enzyme kinetics
Feature tables	Feature tables
Information	Information
Nucleic 2d structure	Nucleic 2d structure
Nucleic codon usage	Nucleic codon usage
Nucleic composition	Nucleic composition
Nucleic cpg islands	Nucleic cpg islands
Nucleic gene finding	Nucleic gene finding
Nucleic motifs	Nucleic motifs
Nucleic mutation	Nucleic mutation
Nucleic primers	Nucleic primers
Nucleic profiles	Nucleic profiles
Nucleic repeats	Nucleic repeats
Nucleic restriction	Nucleic restriction
Nucleic transcription	Nucleic transcription
Nucleic translation	Nucleic translation
Phylogeny distance matrix	Phylogeny distance matrix
Protein 2d structure	Protein 2d structure
Protein 3d structure	Protein 3d structure
Protein composition	Protein composition
Protein motifs	Protein motifs
Protein mutation	Protein mutation
Protein profiles	Protein profiles
Protein sequence alignment	Protein sequence alignment
Utils database creation	Utils database creation
Utils database indexing	Utils database indexing
Utils misc	Utils misc

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

EMBASSY - DOMAINATRIX

EMBASSY - OTHERS