EMBOSS European Molecular Biology Open Software Suite

• EMBOSS programs take parameters or qualifiers in the UNIX style, but with extra flexibility.
  • for example "-consensus" or "-noconsensus".
  • if a value is required then "-sbegin 25" or "-sbegin=25".
  • the qualifiers are words, not single letters, but they can be abbreviated.
  • they are not case sensitive.
  • more details are at the EMBOSS command line page.

• To access sequences, EMBOSS uses a Uniform Sequence Address, or USA, such as:
  • "filename" - a file in any format.
  • "filename:seq1" - for the seq1 in filename which contains several sequences.
  • "dbname:seq1" - as above but dbname is the name of a database.
  • "format::filename" - filename, which is in the specified format (e.g. FASTA).
  • "@listfilename" - list filename contains several USA entries.
  • one : separates a file or database name from a sequence entry name.
  • two :: separate a file format from a file name.

Program name	Author(s)	Description
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
chaos	Sanger	Create a chaos plot for a sequence.
checktrans	EBI	ORF property statistics
chips	HGMP	Codon usage statistics
cirdna	Norway	Draws circular maps of DNA constructs
cluster	Sanger	DNA sequence clustering
codcmp	HGMP	Codon usage table comparison
complex	EMBnet Italy	Find the linguistic complexity in nucleotide sequences
compseq	HGMP	Counts the composition of dimer/trimer/etc words in a sequence
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
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
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
emma	HGMP	Multiple alignment program
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.
iep	HGMP	Calculates the isoelectric point of a protein
infoseq	HGMP	Displays some simple information about sequences
isochore	Sanger	Plots isochores in large DNA sequences
lindna	Norway	Draws linear maps of DNA constructs
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
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
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
redata	HGMP	Isoschizomers, references and Suppliers for Restriction Enzymes
remap	HGMP	Display a sequence with restriction cut sites, translation etc..
restrict	HGMP	Finds Restriction Enzyme Cleavage Sites
revseq	HGMP	Reverse and complement a sequence.
seealso	HGMP	Finds programs sharing group names
seqmatchall	Sanger	Sequence comparison
seqret	Sanger	Reads and writes (returns) a sequence.
seqretall	Sanger	Reads and writes (returns) a set of sequences one at a time.
seqretset	Sanger	Reads and writes (returns) a set of sequences all at once.
showdb	HGMP	Displays information on the currently available databases
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.
splitter	HGMP	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	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.
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.

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