Welcome to EMBOSS explorer, a graphical user interface to the EMBOSS suite of bioinformatics tools.
To continue, select an application from the menu to the left. Move the mouse pointer over the name of an application in the menu to display a short description. To search for a particular application, use wossname.
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.
Within EMBOSS are more than 100 programs. Some of the areas covered are:
There is a large overlap in the functionality available in EMBOSS and the commercial GCG (Wisconsin Package). The following table is a mapping between the programs of the two packages. Much of the content of this section was originally conceived at Helix Systems, CIT, NIH (http://helix.nih.gov/) and the Computational Biology Research Group at Oxford University.
Please direct any questions and comments to slesniak@bioinfo.ucr.edu.
| | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | Y | | |||
| Application | Description | GCG equivalent | Documentation |
|---|---|---|---|
| aaindexextract | Extract data from AAINDEX | - | aaindexextract manual |
| abiview | Reads ABI file and display the trace | - | abiview manual |
| allversusall | Sequence similarity data from all-versus-all comparison | - | allversusall manual |
| antigenic | Finds antigenic sites in proteins | - | antigenic manual |
| backtranseq | Back translate a protein sequence | BackTranslate | backtranseq manual |
| banana | Bending and curvature plot in B-DNA | - | banana manual |
| biosed | Replace or delete sequence sections | Replace | biosed manual |
| btwisted | Calculates the twisting in a B-DNA sequence | - | btwisted manual |
| cai | CAI codon adaptation index | - | cai manual |
| cathparse | Generates DCF file from raw CATH files | - | cathparse manual |
| chaos | Create a chaos game representation plot for a sequence | - | chaos manual |
| charge | Protein charge plot | - | charge manual |
| checktrans | Reports STOP codons and ORF statistics of a protein | - | checktrans manual |
| chips | Codon usage statistics | CodonFrequency | chips manual |
| cirdna | Draws circular maps of DNA constructs | PlasmidMap | cirdna manual |
| codcmp | Codon usage table comparison | Correspond | codcmp manual |
| codcopy | Reads and writes a codon usage table | - | codcopy manual |
| coderet | Extract CDS, mRNA and translations from feature tables | - | coderet manual |
| compseq | Count composition of dimer/trimer/etc words in a sequence | CodonFrequency, Composition | compseq manual |
| cons | Creates a consensus from multiple alignments | Pretty | cons manual |
| contacts | Generate intra-chain CON files from CCF files | - | contacts manual |
| cpgplot | Plot CpG rich areas | - | cpgplot manual |
| cpgreport | Reports all CpG rich regions | - | cpgreport manual |
| cusp | Create a codon usage table | CodonFrequency | cusp manual |
| cutgextract | Extract data from CUTG | - | cutgextract manual |
| cutseq | Removes a specified section from a sequence | seqed | cutseq manual |
| dan | Calculates DNA RNA/DNA melting temperature | MeltTemp | dan manual |
| dbiblast | Index a BLAST database | DataSet | dbiblast manual |
| dbifasta | Database indexing for fasta file databases | - | dbifasta manual |
| dbiflat | Index a flat file database | DataSet | dbiflat manual |
| dbigcg | Index a GCG formatted database | DataSet | dbigcg manual |
| dbxfasta | Database b+tree indexing for fasta file databases | - | dbxfasta manual |
| dbxflat | Database b+tree indexing for flat file databases | - | dbxflat manual |
| dbxgcg | Database b+tree indexing for GCG formatted databases | - | dbxgcg manual |
| degapseq | Removes gap characters from sequences | Replace, seqed | degapseq manual |
| descseq | Alter the name or description of a sequence | - | descseq manual |
| diffseq | Find differences between nearly identical sequences | NoOverlap | diffseq manual |
| digest | Protein proteolytic enzyme or reagent cleavage digest | Peptidemap | digest manual |
| distmat | Creates a distance matrix from multiple alignments | - | distmat manual |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file | - | domainalign manual |
| domainer | Generates domain CCF files from protein CCF files | - | domainer manual |
| domainnr | Removes redundant domains from a DCF file | - | domainnr manual |
| domainrep | Reorder DCF file to identify representative structures | - | domainrep manual |
| domainreso | Remove low resolution domains from a DCF file | - | domainreso manual |
| domainseqs | Adds sequence records to a DCF file | - | domainseqs manual |
| domainsse | Add secondary structure records to a DCF file | - | domainsse manual |
| dotmatcher | Displays a thresholded dotplot of two sequences | DotPlot, Compare | dotmatcher manual |
| dotpath | Non-overlapping wordmatch dotplot of two sequences | - | dotpath manual |
| dottup | Displays a wordmatch dotplot of two sequences | DotPlot, Compare | dottup manual |
| dreg | Regular expression search of a nucleotide sequence | Findpatterns | dreg manual |
| einverted | Finds DNA inverted repeats | Repeat | einverted manual |
| embossdata | Finds or fetches data files read by EMBOSS programs | - | embossdata manual |
| embossversion | Writes the current EMBOSS version number | - | embossversion manual |
| emma | Multiple alignment program - interface to ClustalW program | - | emma manual |
| emowse | Protein identification by mass spectrometry | - | emowse manual |
| entret | Reads and writes (returns) flatfile entries | - | entret manual |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites | - | epestfind manual |
| eprimer3 | Picks PCR primers and hybridization oligos | Prime | eprimer3 manual |
| equicktandem | Finds tandem repeats | Repeat | equicktandem manual |
| esim4 | Align an mRNA to a genomic DNA sequence | - | esim4 manual |
| est2genome | Align EST and genomic DNA sequences | - | est2genome manual |
| etandem | Looks for tandem repeats in a nucleotide sequence | StemLoop, Repeat | etandem manual |
| extractfeat | Extract features from a sequence | - | extractfeat manual |
| extractseq | Extract regions from a sequence | Sample | extractseq manual |
| fclique | Largest clique program | - | fclique manual |
| fconsense | Majority-rule and strict consensus tree | - | fconsense manual |
| fcontml | Gene frequency and continuous character Maximum Likelihood | - | fcontml manual |
| fcontrast | Continuous character Contrasts | - | fcontrast manual |
| fdiscboot | Bootstrapped discrete sites algorithm | - | fdiscboot manual |
| fdnacomp | DNA compatibility algorithm | - | fdnacomp manual |
| fdnadist | Nucleic acid sequence Distance Matrix program | - | fdnadist manual |
| fdnainvar | Nucleic acid sequence Invariants method | - | fdnainvar manual |
| fdnaml | Estimates nucleotide phylogeny by maximum likelihood | - | fdnaml manual |
| fdnamlk | Estimates nucleotide phylogeny by maximum likelihood | - | fdnamlk manual |
| fdnamove | Interactive DNA parsimony | - | fdnamove manual |
| fdnapars | DNA parsimony algorithm | - | fdnapars manual |
| fdnapenny | Penny algorithm for DNA | - | fdnapenny manual |
| fdollop | Dollo and polymorphism parsimony algorithm | - | fdollop manual |
| fdolmove | Interactive Dollo or Polymorphism Parsimony | - | fdolmove manual |
| fdolpenny | Penny algorithm Dollo or polymorphism | - | fdolpenny manual |
| fdrawgram | Plots a cladogram- or phenogram-like rooted tree diagram | - | fdrawgram manual |
| fdrawtree | Plots an unrooted tree diagram | - | fdrawtree manual |
| ffactor | Multistate to binary recoding program | - | ffactor manual |
| ffitch | Fitch-Margoliash and Least-Squares Distance Methods | - | ffitch manual |
| ffreqboot | Bootstrapped genetic frequencies algorithm | - | ffreqboot manual |
| fgendist | Compute genetic distances from gene frequencies | - | fgendist manual |
| findkm | Find Km and Vmax for an enzyme reaction | - | findkm manual |
| fkitsch | Fitch-Margoliash method with contemporary tips | - | fkitsch manual |
| fmix | Mixed parsimony algorithm | - | fmix manual |
| fmove | Interactive mixed method parsimony | - | fmove manual |
| fneighbor | Phylogenies from distance matrix by N-J or UPGMA method | - | fneighbor manual |
| fpars | Discrete character parsimony | - | fpars manual |
| fpenny | Penny algorithm, branch-and-bound | - | fpenny manual |
| fproml | Protein phylogeny by maximum likelihood | - | fproml manual |
| fpromlk | Protein phylogeny by maximum likelihood | - | fpromlk manual |
| fprotdist | Protein distance algorithm | - | fprotdist manual |
| fprotpars | Protein pasimony algorithm | - | fprotpars manual |
| freak | Residue/base frequency table or plot | Window + Statplot | freak manual |
| frestboot | Bootstrapped restriction sites algorithm | - | frestboot manual |
| frestdist | Distance matrix from restriction sites or fragments | - | frestdist manual |
| frestml | Restriction site maximum Likelihood method | - | frestml manual |
| fretree | Interactive tree rearrangement | - | fretree manual |
| fseqboot | Bootstrapped sequences algorithm | - | fseqboot manual |
| fseqbootall | Bootstrapped sequences algorithm | - | fseqbootall manual |
| ftreedist | Distances between trees | - | ftreedist manual |
| ftreedistpair | Distances between two sets of trees | - | ftreedistpair manual |
| fuzznuc | Nucleic acid pattern search | FindPatterns | fuzznuc manual |
| fuzzpro | Protein pattern search | FindPatterns | fuzzpro manual |
| fuzztran | Protein pattern search after translation | - | fuzztran manual |
| garnier | Predicts protein secondary structure | Peptidestructure | garnier manual |
| geecee | Calculates fractional GC content of nucleic acid sequences | - | geecee manual |
| getorf | Finds and extracts open reading frames (ORFs) | Pepdata | getorf manual |
| helixturnhelix | Report nucleic acid binding motifs | HTHScan | helixturnhelix manual |
| hetparse | Converts heterogen group dictionary to EMBL-like format | - | hetparse manual |
| hmoment | Hydrophobic moment calculation | - | hmoment manual |
| iep | Calculates the isoelectric point of a protein | Isoelectric | iep manual |
| infoalign | Information on a multiple sequence alignment | - | infoalign manual |
| infoseq | Displays some simple information about sequences | Names | infoseq manual |
| interface | Generate inter-chain CON files from CCF files | - | interface manual |
| isochore | Plots isochores in large DNA sequences | - | isochore manual |
| libgen | Generate discriminating elements from alignments | - | libgen manual |
| lindna | Draws linear maps of DNA constructs | PlasmidMap | lindna manual |
| listor | Write a list file of the logical OR of two sets of sequences | - | listor manual |
| marscan | Finds MAR/SAR sites in nucleic sequences | - | marscan manual |
| maskfeat | Mask off features of a sequence | - | maskfeat manual |
| maskseq | Mask off regions of a sequence | Seg | maskseq manual |
| matcher | Finds the best local alignments between two sequences | BestFit | matcher manual |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files | - | matgen3d manual |
| megamerger | Merge two large overlapping nucleic acid sequences | - | megamerger manual |
| merger | Merge two overlapping nucleic acid sequences | Assemble | merger manual |
| msbar | Mutate sequence beyond all recognition | Corrupt | msbar manual |
| mwcontam | Shows molwts that match across a set of files | - | mwcontam manual |
| mwfilter | Filter noisy molwts from mass spec output | - | mwfilter manual |
| needle | Needleman-Wunsch global alignment | Gap | needle manual |
| newcpgreport | Report CpG rich areas | - | newcpgreport manual |
| newcpgseek | Reports CpG rich regions | - | newcpgseek manual |
| newseq | Type in a short new sequence | - | newseq manual |
| noreturn | Removes carriage return from ASCII files | - | noreturn manual |
| notseq | Exclude a set of sequences and write out the remaining ones | - | notseq manual |
| nthseq | Writes one sequence from a multiple set of sequences | Reformat | nthseq manual |
| octanol | Displays protein hydropathy | Moment | octanol manual |
| oddcomp | Find protein sequence regions with a biased composition | - | oddcomp manual |
| palindrome | Looks for inverted repeats in a nucleotide sequence | StemLoop, Repeat | palindrome manual |
| pasteseq | Insert one sequence into another | - | pasteseq manual |
| patmatdb | Search a protein sequence with a motif | Profilescan | patmatdb manual |
| patmatmotifs | Search a PROSITE motif database with a protein sequence | Motifs | patmatmotifs manual |
| pdbparse | Parses PDB files and writes protein CCF files | - | pdbparse manual |
| pdbplus | Add accessibility & secondary structure to a CCF file | - | pdbplus manual |
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format | - | pdbtosp manual |
| pepcoil | Predicts coiled coil regions | CoilScan | pepcoil manual |
| pepinfo | Plots simple amino acid properties in parallel | Pepplot | pepinfo manual |
| pepnet | Displays proteins as a helical net | Moment | pepnet manual |
| pepstats | Protein statistics | Composition | pepstats manual |
| pepwheel | Shows protein sequences as helices | HelicalWheel | pepwheel manual |
| pepwindow | Displays protein hydropathy | - | pepwindow manual |
| pepwindowall | Displays protein hydropathy of a set of sequences | - | pepwindowall manual |
| plotcon | Plot quality of conservation of a sequence alignment | Gapshow, PlotSimilarity | plotcon manual |
| plotorf | Plot potential open reading frames | Frames | plotorf manual |
| polydot | Displays all-against-all dotplots of a set of sequences | - | polydot manual |
| preg | Regular expression search of a protein sequence | - | preg manual |
| prettyplot | Displays aligned sequences, with colouring and boxing | prettybox | prettyplot manual |
| prettyseq | Output sequence with translated ranges | - | prettyseq manual |
| primersearch | Searches DNA sequences for matches with primer pairs | PrimePair | primersearch manual |
| printsextract | Extract data from PRINTS | - | printsextract manual |
| profit | Scan a sequence or database with a matrix or profile | Profilesearch, Motifsearch | profit manual |
| prophecy | Creates matrices/profiles from multiple alignments | Consensus, Profilegap, Meme | prophecy manual |
| prophet | Gapped alignment for profiles | Profilemake | prophet manual |
| prosextract | Build the PROSITE motif database for use by patmatmotifs | - | prosextract manual |
| pscan | Scans proteins using PRINTS | - | pscan manual |
| psiphi | Phi and psi torsion angles from protein coordinates | - | psiphi manual |
| rebaseextract | Extract data from REBASE | - | rebaseextract manual |
| recoder | Remove restriction sites but maintain same translation | - | recoder manual |
| redata | Search REBASE for enzyme name, references, suppliers etc | redata manual | |
| remap | Display sequence with restriction sites, translation etc | Mapsort, Map, Mapplot | remap manual |
| restover | Find restriction enzymes producing specific overhang | Mapsort, Map, Mapplot | restover manual |
| restrict | Finds restriction enzyme cleavage sites | Mapsort, Map, Mapplot | restrict manual |
| revseq | Reverse and complement a sequence | Reverse | revseq manual |
| rocon | Generates a hits file from comparing two DHF files | - | rocon manual |
| rocplot | Performs ROC analysis on hits files | - | rocplot manual |
| scopparse | Generate DCF file from raw SCOP files | - | scopparse manual |
| seealso | Finds programs sharing group names | - | seealso manual |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) | - | seqalign manual |
| seqfraggle | Removes fragment sequences from DHF files | - | seqfraggle manual |
| seqmatchall | All-against-all comparison of a set of sequences | - | seqmatchall manual |
| seqnr | Removes redundancy from DHF files | - | seqnr manual |
| seqret | Reads and writes (returns) sequences | ToFastA, Reformat, Fetch, Publish, Getseq | seqret manual |
| seqretsplit | Reads and writes (returns) sequences in individual files | Fetch | seqretsplit manual |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file | - | seqsearch manual |
| seqsort | Remove ambiguous classified sequences from DHF files | - | seqsort manual |
| seqwords | Generates DHF files from keyword search of UniProt | - | seqwords manual |
| showalign | Displays a multiple sequence alignment | prettybox | showalign manual |
| showdb | Displays information on the currently available databases | - | showdb manual |
| showfeat | Show features of a sequence | - | showfeat manual |
| showorf | Pretty output of DNA translations | Frames | showorf manual |
| showseq | Display a sequence with features, translation etc | Publish | showseq manual |
| shuffleseq | Shuffles a set of sequences maintaining composition | Shuffle | shuffleseq manual |
| sigcleave | Reports protein signal cleavage sites | SPScan | sigcleave manual |
| siggen | Generates a sparse protein signature from an alignment | - | siggen manual |
| siggenlig | Generate ligand-binding signatures from a CON file | - | siggenlig manual |
| sigscan | Generate hits (DHF file) from a signature search | - | sigscan manual |
| sigscanlig | Search ligand-signature library & write hits (LHF file) | - | sigscanlig manual |
| silent | Silent mutation restriction enzyme scan | - | silent manual |
| sirna | Finds siRNA duplexes in mRNA | - | sirna manual |
| sites | Generate residue-ligand CON files from CCF files | - | sites manual |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs | Pepdata | sixpack manual |
| skipseq | Reads and writes (returns) sequences, skipping first few | - | skipseq manual |
| splitter | Split a sequence into (overlapping) smaller sequences | Breakup | splitter manual |
| ssematch | Search a DCF file for secondary structure matches | - | ssematch manual |
| stretcher | Finds the best global alignment between two sequences | Gap | stretcher manual |
| stssearch | Search a DNA database for matches with a set of STS primers | - | stssearch manual |
| supermatcher | Match large sequences against one or more other sequences | - | supermatcher manual |
| syco | Synonymous codon usage Gribskov statistic plot | CodonPreference | syco manual |
| tcode | Fickett TESTCODE statistic to identify protein-coding DNA | - | tcode manual |
| textsearch | Search sequence documentation. Slow, use SRS and Entrez! | Stringsearch | textsearch manual |
| tfextract | Extract data from TRANSFAC | - | tfextract manual |
| tfm | Displays a program's help documentation manual | gcghelp | tfm manual |
| tfscan | Scans DNA sequences for transcription factors | - | tfscan manual |
| tmap | Displays membrane spanning regions | - | tmap manual |
| topo | Draws an image of a transmembrane protein | - | topo manual |
| tranalign | Align nucleic coding regions given the aligned proteins | - | tranalign manual |
| transeq | Translate nucleic acid sequences | Translate, ExtractPeptide | transeq manual |
| trimest | Trim poly-A tails off EST sequences | - | trimest manual |
| trimseq | Trim ambiguous bits off the ends of sequences | - | trimseq manual |
| twofeat | Finds neighbouring pairs of features in sequences | - | twofeat manual |
| union | Reads sequence fragments and builds one sequence | - | union manual |
| vectorstrip | Strips out DNA between a pair of vector sequences | - | vectorstrip manual |
| water | Smith-Waterman local alignment | BestFit | water manual |
| whichdb | Search all databases for an entry | - | whichdb manual |
| wobble | Wobble base plot | CodonPreference, Testcode | wobble manual |
| wordcount | Counts words of a specified size in a DNA sequence | - | wordcount manual |
| wordmatch | Finds all exact matches of a given size between 2 sequences | - | wordmatch manual |
| wossname | Finds programs by keywords in their one-line documentation | - | wossname manual |
| yank | Reads a sequence range, appends the full USA to a list file | - | yank manual |
For more information about EMBOSS explorer, including how to download and install it locally, visit the EMBOSS explorer website.
Development of EMBOSS explorer has been supported by the National Research Council of Canada and Genome Prairie.