EMBOSS: The Applications (programs)

The programs are listed in alphabetical order, divided into four sections. Look at the individual applications or go to the GROUPS page.

• Current release
• EMBASSY
• Proposed

Applications in the current release

Description

abiview	HGMP	Reads ABI file and display the trace
acdc	Sanger	Tests definition files for any EMBOSS application.
antigenic	HGMP	Finds antigenic sites in proteins
backtranseq	HGMP	Back translate a protein sequence
banana	Sanger	Bending and Curvature Plot in B-DNA
btwisted	HGMP	Calculates the twisting in a B-DNA sequence
cai	HGMP	CAI codon usage statistic
chaos	Sanger	Create a chaos plot for a sequence.
charge	HGMP	Protein charge plot
checktrans	EBI	ORF property statistics
chips	HGMP	Codon usage statistics
cirdna	Norway	Draws circular maps of DNA constructs
codcmp	HGMP	Codon usage table comparison
coderet	HGMP	Extract CDS, mRNA and translations from feature tables
compseq	HGMP	Counts the composition of dimer/trimer/etc words in a sequence
contacts	HGMP	Reads coordinate files and writes contact files
cons	HGMP	Creates a consensus from multiple alignments
cpgplot	HGMP	Plot CpG rich areas
cpgreport	HGMP	Reports CpG rich regions
cusp	HGMP	Create a codon usage table
cutseq	HGMP	Removes a specified section from a sequence.
dan	HGMP	Plot melting temperatures for DNA.
dbiblast	Sanger	Database indexing for BLAST 1 and 2 indexed databases
dbifasta	HGMP	Index a fasta database
dbiflat	Sanger	Database indexing for flat file databases
dbigcg	Sanger	Database indexing for GCG formatted databases
degapseq	HGMP	Removes gap characters from sequences
descseq	HGMP	Alter the name or description of a sequence.
diffseq	HGMP	Find differences (SNPs) between nearly identical sequences
digest	HGMP	Protein proteolytic enzyme or reagent cleavage digest
distmat	HGMP	Creates a distance matrix from multiple alignments
domainer	HGMP	Build domain coordinate files
dotmatcher	Sanger	Produces a dotplot of two sequences.
dotpath	HGMP	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	HGMP	Finds or fetches the data files read in by the EMBOSS programs
embossversion	HGMP	Writes the current EMBOSS version number
emowse	HGMP	Protein identification by mass spectrometry
emma	HGMP	Multiple alignment program
entret	HGMP	Reads and writes (returns) flatfile entries
equicktandem	Sanger	Finds tandem repeats
est2genome	Sanger	Align EST and genomic DNA sequences
etandem	Sanger	Looks for tandem repeats in a nucleotide sequence.
extractseq	HGMP	Extract regions from a sequence.
findkm	HGMP	Calculates Km and Vmax for an enzyme reaction
freak	HGMP	Residue/base frequency table or plot
fuzznuc	HGMP	Nucleic acid pattern search
fuzzpro	HGMP	Protein pattern search
fuzztran	HGMP	Protein pattern search after translation
garnier	EBI	Predicts protein secondary structure
geecee	Sanger	Calculates the fractional GC content of nucleic acid sequences
getorf	HGMP	Finds and extracts open reading frames (ORFs)
helixturnhelix	HGMP	Finds nucleic acid binding domains.
hmoment	HGMP	Hydrophobic moment calculation
iep	HGMP	Calculates the isoelectric point of a protein
infoalign	HGMP	Information on a multiple sequence alignment
infoseq	HGMP	Displays some simple information about sequences
isochore	Sanger	Plots isochores in large DNA sequences
lindna	Norway	Draws linear maps of DNA constructs
listor	HGMP	Writes a list file of the logical OR of two sets of sequences
marscan	HGMP	Finds MAR/SAR sites in nucleic sequences
maskfeat	HGMP	Mask off features of a sequence
maskseq	HGMP	Mask off regions of a sequence.
matcher	Sanger	Local alignment of two sequences
megamerger	HGMP	Merge two large overlapping nucleic acid sequences
merger	HGMP	Merge two overlapping sequences
msbar	HGMP	Mutate sequence beyond all recognition
needle	HGMP	Needleman-Wunsch global alignment.
newcpgreport	EBI	Report CpG rich areas
newcpgseek	EBI	Reports CpG rich regions
newseq	HGMP	Type in a short new sequence.
noreturn	HGMP	Removes carriage return from ASCII files
notseq	HGMP	Excludes a set of sequences and writes out the remaining ones
nrscope	HGMP	Converts redundant EMBL-format SCOP file to non-redundant one
nthseq	HGMP	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	HGMP	Looks for inverted repeats in a nucleotide sequence.
pasteseq	HGMP	Insert one sequence into another.
patmatdb	HGMP	Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs	HGMP	Compares a protein sequence to the PROSITE motif database.
pepcoil	HGMP	Predicts coiled coil regions
pepinfo	HGMP	Plots simple amino acid properties in parallel
pepnet	HGMP	Protein helical net plot
pepstats	HGMP	Protein statistics
pepwheel	HGMP	Shows protein sequences as helices
pepwindow	Sanger	Displays protein hydropathy
pepwindowall	Sanger	Displays protein hydropathy of a set of sequences
plotcon	HGMP	Plots the quality of conservation of a sequence alignment
plotorf	HGMP	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	HGMP	Output sequence with translated ranges
prima	HGMP	Selecting primers for PCR and DNA amplification.
primersearch	HGMP	Searches DNA sequences for matches with primer pairs
printsextract	HGMP	Preprocesses the PRINTS database for use with the program PSCAN
profit	HGMP	Scan a sequence or database with a matrix or profile
prophecy	HGMP	Creates matrices/profiles from multiple alignments
prophet	HGMP	Gapped alignment for profiles
prosextract	HGMP	Extracts ID, AC, and PA lines from the PROSITE motif database.
pscan	HGMP	Locates fingerprints (multiple motif features) in a protein sequence.
rebaseextract	HGMP	Extract data from REBASE
recoder	HGMP	Find and remove restriction sites but maintain the same translation
redata	HGMP	Isoschizomers, references and Suppliers for Restriction Enzymes
remap	HGMP	Display a sequence with restriction cut sites, translation etc..
restover	Sloan-Kettering Cancer Center	Finds restriction enzymes that produce a specific overhang
restrict	HGMP	Finds Restriction Enzyme Cleavage Sites
revseq	HGMP	Reverse and complement a sequence.
scopalign	HGMP	Generate alignments for SCOP families
scope	HGMP	Convert raw scop classification file to embl-like format
seealso	HGMP	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.
seqretall	Sanger	Reads and writes (returns) a set of sequences one at a time.
seqretallfeat	HGMP	Reads and writes (returns) one or more sequences
seqretset	Sanger	Reads and writes (returns) a set of sequences all at once.
seqretsplit	HGMP	Reads and writes (returns) sequences in individual files
showdb	HGMP	Displays information on the currently available databases
showalign	HGMP	Display a multiple sequence alignment
showfeat	HGMP	Show features of a sequence.
showorf	HGMP	Pretty output of DNA translations
showseq	HGMP	Display a sequence with features, translation etc
shuffleseq	HGMP	Shuffles a set of sequences maintaining composition
sigcleave	HGMP	Predicts signal peptide cleavage sites
siggen	HGMP	Generates a sparse protein signature
sigscan	HGMP	Scans a sparse protein signature against swissprot
silent	HGMP	Silent mutation restriction enzyme scan
splitter	HGMP	Split a sequence into (overlapping) smaller sequences.
stamps	HGMP	Generate alignments for SCOP families
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	HGMP	Synonymous codon usage Gribskov statistic plot
textsearch	HGMP	Search sequence documentation text. SRS and Entrez are faster!
tfextract	HGMP	Extract data from TRANSFAC
tfm	HGMP	Displays a program's help documentation manual
tfscan	HGMP	Scans DNA sequences for transcription factors.
tmap	Sanger	Predict transmembrane proteins
transeq	HGMP	Translates nucleic acid sequences.
trimest	HGMP	Trim poly-A tails off EST sequences
trimseq	HGMP	Trim ambiguous bits off the ends of sequences
vectorstrip	HGMP	Strips out DNA between a pair of vector sequences
water	HGMP	Smith-Waterman local alignment.
wobble	HGMP	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	HGMP	Finds programs by keywords in their one-line documentation.

EMBASSY