Welcome to EMBOSS explorer, a graphical user interface to the EMBOSS suite of bioinformatics tools.
Not sure which tool to use? Try the bioinformatics FAQ
Please note: you will need your molbiol username and password to use these tools.
| | 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 |
| 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 |