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EMBOSS

EMBOSS is "European Molecular Biology Open Software Suite". It is a free Open Source software analysis package specially developed for the needs of the molecular biology user community.

The EMBOSS suite is available via Unix or online.

Within EMBOSS are more than 100 programs. Some of the areas covered are:

Sequence alignment
Rapid database searching with sequence patterns
Protein motif identification, including domain analysis
Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats
Codon usage analysis for small genomes
Rapid identification of sequence patterns in large scale sequence sets
Presentation tools for publication
And much more...

Run EMBOSS programs online

Go to EMBOSS Explorer.

Comparison between the programs in GCG and EMBOSS

There is a large overlap in the functionality available in EMBOSS and the commercial GCG (Wisconsin Package). This table is a mapping between the programs of the two packages (Full details of all the programs that make up the GCG package can be found here).

Much of the content of this section was originally conceived at Helix Systems, CIT, NIH (http://helix.nih.gov/) and has been reproduced here with kind permission.

GCG program	EMBOSS program	Description/Comments
Assemble	merger	Construct new sequences from pieces of existing sequences; merger only accepts 2 sequences while assemble accepts several.
BackTranslate	backtranseq	Backtranslate protein -> nucleotide sequence
BestFit	water matcher	Bestfit uses the Smith-Waterman algorithm to find the best local alignment between 2 sequences. water uses Smith-Waterman, matcher uses Pearson's lalign algorithm.
BLAST Psiblast	dbiBlast	NCBI homology search between query and database
Breakup	splitter	Splits a sequence into (overlapping) smaller sequences
Chopup	-	Helps to convert a non-GCG sequence format. Not needed in EMBOSS because it reads most sequence formats without conversion
CodonFrequency	chips compseq cusp	CodonFrequency -- tabulates codon usage. compseq -- counts composition of dimer/trimer in sequence. chips -- calculates codon usage stats cusp -- creates a codon usage table.
CodonPreference	syco wobble	Recognize protein coding sequences
CoilScan	pepcoil	Predicts coiled-coil regions
Compare + Dotplot	dottup + dotmatcher	2-sequence comparison
Composition	compseq pepstats	Sequence composition
CompressText	-	Removes extra whitespace in text files. Can be done via Unix shell script.
CompTable	-	Creates a scoring matrix
Consensus	prophecy	Creates a consensus sequence or matrices/profiles from multiple alignments
Correspond	codcmp	Codon usage table comparison
Corrupt	msbar	Randomly mutate sequence
DataSet	dbiflat dbiblast dbigcg	Creates searchable sequence database. GCG's Dataset requires sequences in GCG format, whereas dbiflat, dbiblast, dbigcg will take most formats between them.
Detab	-	Replaces tabs with spaces in sequence files. Can be performed by Unix shell command.
Distances	-	Calculates pairwise evolutionary distances between aligned sequences. The Phylip package can do this.
Diverge	-	Estimates pairwise substitutions per site between 2 or more coding sequences. The Phylip package can do this.
DotPlot	dottup dotmatcher
ExtractPeptide	transeq	ExtractPeptide takes the output of Map and can write one or more of the reading-frame translations. transeq translates one or more of the frames or specific regions directly from an input nucleotide sequence.
FastA FastX Tfasta TfastX	-	Pearson's homology-search program, available as a standalone program on molbiol.
Fetch	seqret seqretsplit	Pull one or more sequences out of the databases. seqret/seqretsplit can save output in various sequence formats.
Figure	-	Generates plots from other GCG programs.
FindPatterns	fuzznuc fuzzpro	searches for patterns in a sequence or database
FingerPrint	-	Finds the products of T1 ribonuclease digestion.
FitConsensus	-	Use after Consensus to find the best fits.
FrameAlign	-	Finds best local alignment including frame shifts between a protein and nucleotide sequence.
Frames	plotorf showorf	Show open reading frames. plotorf does this graphically
Framesearch	-	Homology searches including frameshifts between protein and nucleotide sequences
FromEMBL FromFasta FromGenbank FromIG FromPIR FromStaden Fromtrace	-	Converts from various formats to GCG sequence format. Unnecessary in EMBOSS because it can accept most sequence formats, but seqret can convert between formats if desired.
Gap	needle stretcher	Needleman-Wunsch algorithm to compare 2 sequences. stretcher uses the Myers-Miller algorithm which is more memory-efficient.
Gapshow	plotcon	Graphical representation of similarity of 2 sequences.
GCGtoBlast	-	Makes a BLAST database. Use NCBI's 'formatdb' instead.
GelAssemble GelDisassemble GelEnter GelMerge GelStart GelView	megamerger merger union	Parts of GCG's gel assembly suite.
Getseq	seqret	Type in a new sequence
Growtree	-	Creates phylogenetic tree. Can use Phylip or Clustal instead.
HelicalWheel	pepwheel	Plots peptide sequence as helical wheel to help recognize amphiphilic regions.
HmmerAlign HmmerBuild HmmerCalibrate HmmerEmit HmmerFetch HmmerIndex HmmerPfam HmmerSearch	-	The HMMER package is available on molbiol.
HTHScan	helixturnhelix	Finds HTH motifs in protein sequences.
Isoelectric	iep	Calculates isoelectric point of a protein.
Lineup	-	Edits multiple sequence alignments
Listfile	-	for printing. Can use Unix psprint command instead.
Lookup	-	Versatile program for finding sequences in a database. "whichdb" in EMBOSS can search for accession numbers, but lookup is much more sophisticated. Can use NCBI tool at http://www.ncbi.nlm.nih.gov/
Map Mapplot Mapsort	restrict remap restover	finds restriction enzyme cleavage sites.
MeltTemp	dan	Computes melting temperature of oligos
MEME	-	Finds conserved motifs in a group of unaligned sequences.
MFold	-	Predicts nucleotide secondary structure. GCG's version is an old version of Zuker's MFOLD.
Moment	pepnet octanol	Makes a contour plot of the helical hydrophobic moment of a peptide sequence
Motifs	patmatmotifs	Finds common Prosite motifs in a sequence. Note that not all Prosite motifs will be found due to a bug in the GCG and EMBOSS programs. Use Interproscan instead (http://www.ebi.ac.uk/InterProScan/)
Meme + Motifsearch	prophecy + profit	Search a sequence or database with a matrix or profile.
Names	infoseq	provides some info about sequence specifications.
NetBlast Netfetch	-	remote access to NCBI's Blast. Use standalone BLAST on molbiol instead.
NoOverlap	diffseq	Finds differences between 2 sequences. NoOverlap can work with a group of sequences.
OldDistances	-	Makes a table of the pairwise similarities within a group of sequenes.
onecase	-	converts sequence into lower or upper case. Can be performed by Unix shell command.
Overlap	-	Compares 2 sets of sequences using Wilbur-Lipman algorithm.
Paupdisplay Paupsearch	-	PAUP Phylogenetic Analysis.
Pepdata	getorf sixpack	Translates in all 6 reading frames. sixpack displays the DNA sequence with 6-frame translations and orfs.
Pepplot	pepinfo	Pepplot plots protein 2ndary structure and hydrophobicity. pepinfo plots hydrophobicity, and garnier does protein 2ndary structure prediction.
Peptidemap	digest	Enzyme/reagent cleavage map of a protein.
Peptidesort	-	Sorts fragments from an enzyme/reagent cleavage of a protein according to position, mol. wt., and HPLC retention.
Peptidestructure Plotstructure	garnier	Secondary structure prediction.
Pileup	(emma)	Multiple sequence alignment. ("emma" interface to the clustalw alignment program. Can also use the standalone Clustal on molbiol, or ClustalW at the EBI.)
PlasmidMap	cirdna lindna	Plot DNA constructs.
PlotFold	-	Plots MFold output.
PlotSimilarity	plotcon	Graphical representation of the similarity along a set of aligned sequences.
Pretty prettybox	cons prettyplot showalign	Calculates consensus sequence from a multiple sequence alignment, and displays them prettily.
Prime	eprimer3	Selects oligonucleotide primers.
Profilegap Profilemake	prophecy prophet	Creates matrices/profiles from multiple alignments. Gapped alignment for profiles and sequences.
PrimePair	primersearch	Evaluates individual primers to determine their compatibility for use as PCR primer pairs.
Profilescan	patmatdb	Searches sequences or db for protein motifs. Profilescan uses Gribskov method.
Profilesearch	profit	Scans a sequence or database with a matrix or profile.
Profilesegments	-	Alignments for results of Profilesearch
Publish	seqret showseq	Makes publication-quality displays of sequences.
Reformat	seqret	GCG requires input sequences to be in GCG format, hence other formats need to be converted with 'reformat'. EMBOSS programs accept most sequence formats, but 'seqret' can be used to convert between formats if desired.
Repeat	equicktandem etandem einverted palindrome	Finds tandem repeats in sequences. The equivalent group of EMBOSS programs will also look for inverted or palindromic repeats.
Replace	biosed degapseq	Replaces characters in a text file. Degapseq is specific for replacing gap characters. Can be performed with Unix shell utilities like sed, awk or tr.
Reverse	revseq	Reverse/complement a sequence.
Sample	extractseq	Extract regions from a sequence.
Seg	maskseq	Masks off low-complexity regions from a sequence.
Seqed	biosed cutseq degapseq descseq entret extractfeat extractseq listor maskfeat maskseq newseq noreturn notseq nthseq pasteseq revseq seqret seqretsplit skipseq splitter trimest trimseq union vectorstrip yank	Sequence editor. EMBOSS has many tools for specific editting tasks. Or use a text editor (but not a word processor).
SeqLab	-	X-windows interface to GCG.
Setkeys	-	Redefines keyboard keys, mainly used for GCG's gel assembly programs.
Shiftover	-	Moves text by column. Use the Unix nedit editor instead.
Shuffle	shuffleseq	Shuffles a sequence.
Simplify	-	Reduce the number of symbols in a sequence.
Spew	-	Sends a sequence from a remote computer to your desktop. Oldfashioned way of file transfer, rarely used now.
SPScan	sigcleave	Predicts signal peptides in protein sequences.
Ssearch	-	Part of Pearson's Fasta package, available as a standalone program on molbiol.
StatPlot	-	Plotting program. Rarely used.
StemLoop	palindrome etandem	Finds inverted repeats.
Stringsearch	textsearch	Finds text phrases in sequence or database. Use NCBI Entrez instead.
Terminator	-	searches for prokaryotic factor-independent RNA polymerase terminators according to the method of Brendel and Trifonov.
Testcode	wobble	Plots 3rd-position variability as an indicator of potential coding regions.
ToFastA ToIG ToPIR ToStaden	seqret	EMBOSS accepts most sequence formats, therefore format conversion is rarely required.
Translate	transeq	Translates nucleotide -> Protein sequences
Transmem	-	predicts transmembrane helices.
Window + Statplot	freak	Residue/base frequency table or plot.
Wordsearch/Segments	-	Homology search using Wilbur/Lipman algorithm. Segments displays the result.
Xnu	-	Masks tandem repeats for future BLAST search. Available as a standalone program on molbiol
-	abiview	Reads ABI file and displays trace
-	antigenic	Finds antigenic sites in proteins
-	banana	Bending and curvature plot in B-DNA
-	btwisted	Calculates the twisting in a B-DNA sequence
-	cai	CAI codon adaptation index, to measure synonymous codon usage bias.
-	chaos	Create a chaos game representation plot for a sequence
-	charge	Protein charge plot.
-	checktrans	Reports STOP codons and ORF statistics of a protein
-	coderet	Extract CDS, mRNA and translations from feature tables
-	cpgplot cpgreport newcpgreport newcpgseek	Plots and reports CpG-rich regions.
seqed	cutseq	Removes a specified section from a sequence. seqed is interactive, cutseq is command-line.
seqed	degapseq	Alter name/description of sequence.
Findpatterns	dreg	Regular expression search of a sequence. Findpatterns is an approximate equivalent.
-	emowse	Protein identification by Mass spectrometry.
-	est2genome	Align EST and genomic DNA sequences.
-	extractfeat	Extract features from a sequence.
-	findkm	Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot
-	fuzztran	Protein pattern search after translation
-	geecee	Calculates the fractional GC content of nucleic acid sequences
-	isochore	Plots isochores in large DNA sequences
-	listor	Writes a list file of the logical OR of two sets of sequences
-	marscan	Finds MAR/SAR sites in nucleic sequences
-	maskfeat	Mask off features of a sequence.
-	mwcontam	Shows mol wts that match across a set of files
-	mwfilter	Filter noisy mol wts from mass spec output
-	noreturn	remove carriage return from a ASCII files. Can be performed by Unix utilities like 'tr'.
Reformat	nthseq	Pulls one sequence out of a multiple set. Reformat will pull a sequence out of an MSF or RSF file.
-	oddcomp	Finds protein sequence regions with a biased composition
-	pestfind	Finds PEST motifs as potential proteolytic cleavage sites
-	polydot	Displays all-against-all dotplots of a set of sequences
-	printsextract	Extract data from PRINTS
-	pscan	Scans proteins using PRINTS
-	rebaseextract redata	Search and extract from REBASE.
-	recoder	Remove restriction sites but maintain the same translation
-	seqmatchall	all-against-all comparison of a set of sequences.
-	showdb	Shows info about currently available databases.
-	showfeat	Shows features of a sequence
-	silent	Silent mutation restriction enzyme scan
-	sirna	Finds siRNA duplexes in mRNA
-	stssearch	Searches a DNA database for matches with a set of STS primers
-	supermatcher	Finds a match of a large sequence against one or more sequences
-	tfextract	Extract data from TRANSFAC database.
gcghelp	tfm	shows documentation for a program.
-	tfscan	Scans DNA sequences for transcription factors
-	tmap	Displays membrane spanning regions
-	tranalign	Align nucleic coding regions given the aligned proteins
-	trimest trimseq	Trim bits off ends of sequences. Can be done interactively with GCG's seqed.
-	twofeat	finds neighbouring pairs of features in sequences
-	vectorstrip	Strips out DNA between a pair of vector sequences
-	wordcount	Counts words of a specified size in a DNA sequence
-	wordmatch	Finds all exact matches of a given size between 2 sequences

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This file last modified Friday September 10, 2010
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