Manual pages
Origin: EMBOSS 6.4.0.
| [ Alias ↣ ] Name (section) | Brief |
|---|---|
| aaindexextract(1e) | Extract amino acid property data from AAINDEX. |
| abiview(1e) | Display the trace in an ABI sequencer file. |
| acdc(1e) | Test an application ACD file. |
| acdlog(1e) | Test application ACD file processing and trace data structures. |
| acdpretty(1e) | Correctly reformat an application ACD file. |
| acdrelations(1e) | Add relations: attribute to ACD files. |
| acdtable(1e) | Generate an HTML table of parameters from an application ACD file. |
| acdtrace(1e) | Trace processing of an application ACD file (for testing). |
| acdvalid(1e) | Validate an application ACD file. |
| ajbad(1e) | Test file for ACD parsing. |
| ajfeatest(1e) | Reads and writes (returns) a sequence and its features. |
| ajtest(1e) | Test file for ACD parsing. |
| aligncopy(1e) | Reads and writes alignments. |
| aligncopypair(1e) | Reads and writes pairs from alignments. |
| antigenic(1e) | Finds antigenic sites in proteins. |
| backtranambig(1e) | Back-translate a protein sequence to ambiguous nucleotide sequence. |
| backtranseq(1e) | Back-translate a protein sequence to a nucleotide sequence. |
| banana(1e) | Plot bending and curvature data for B-DNA. |
| biosed(1e) | Replace or delete sequence sections. |
| btwisted(1e) | Calculate the twisting in a B-DNA sequence. |
| cachedas(1e) | Generates server cache file for DAS servers or for the DAS registry. |
| cachedbfetch(1e) | Generates server cache file for Dbfetch/WSDbfetch data sources. |
| cacheebeyesearch(1e) | Generates server cache file for EB-eye search domains. |
| cacheensembl(1e) | Generates server cache file for an Ensembl server. |
| cai(1e) | Calculate codon adaptation index. |
| chaos(1e) | Draw a chaos game representation plot for a nucleotide sequence. |
| charge(1e) | Draw a protein charge plot. |
| checktrans(1e) | Reports STOP codons and ORF statistics of a protein. |
| chips(1e) | Calculates Nc codon usage statistic. |
| cirdna(1e) | Draws circular maps of DNA constructs. |
| codcmp(1e) | Codon usage table comparison. |
| codcopy(1e) | Copy and reformat a codon usage table. |
| coderet(1e) | Extract CDS, mRNA and translations from feature tables. |
| complex(1e) | Find the linguistic complexity in nucleotide sequences. |
| compseq(1e) | Calculate the composition of unique words in sequences. |
| cons(1e) | Create a consensus sequence from a multiple alignment. |
| consambig(1e) | Create an ambiguous consensus sequence from a multiple alignment. |
| corbatest(1e) | Test of EMBL corba retrieval. |
| cpgplot(1e) | Identify and plot CpG islands in nucleotide sequence(s). |
| cpgreport(1e) | Identify and report CpG-rich regions in nucleotide sequence(s). |
| cusp(1e) | Create a codon usage table from nucleotide sequence(s). |
| cutgextract(1e) | Extract codon usage tables from CUTG database. |
| cutseq(1e) | Removes a section from a sequence. |
| dan(1e) | Calculates nucleic acid melting temperature. |
| dastest(1e) | Return DAS sources from a DAS server or from the DAS registry. |
| dbfetchtest(1e) | Generates server cache file for WSDbfetch data sources. |
| dbget(1e) | Retrieve database entries for a named database, data type and data identifier. |
| dbgeturl(1e) | Retrieve links to database entries for a named database, data type and data identifier. |
| dbiblast(1e) | Index a BLAST database. |
| dbifasta(1e) | Index a fasta file database. |
| dbiflat(1e) | Index a flat file database. |
| dbigcg(1e) | Index a GCG formatted database. |
| dbshowdat(1e) | Show possible database queries that return a given data type. |
| dbshowquery(1e) | Show possible database queries that use a given data identifier. |
| dbtell(1e) | Display information about a public database. |
| dbtellquery(1e) | Show possible queries of a database. |
| dbxcompress(1e) | Compress an uncompressed dbx index. |
| dbxedam(1e) | Index the EDAM ontology using b+tree indices. |
| dbxfasta(1e) | Index a fasta file database using b+tree indices. |
| dbxflat(1e) | Index a flat file database using b+tree indices. |
| dbxgcg(1e) | Index a GCG formatted database using b+tree indices. |
| dbxobo(1e) | Index an obo ontology using b+tree indices. |
| dbxreport(1e) | Validate index and report internals for dbx databases. |
| dbxresource(1e) | Index a data resource catalogue using b+tree indices. |
| dbxstat(1e) | Dump statistics for dbx databases. |
| dbxtax(1e) | Index NCBI taxonomy using b+tree indices. |
| dbxuncompress(1e) | Uncompress a compressed dbx index. |
| degapseq(1e) | Removes non-alphabetic (e.g. gap) characters from sequences. |
| density(1e) | Draw a nucleic acid density plot. |
| descseq(1e) | Alter the name or description of a sequence. |
| diffseq(1e) | Compare and report features of two similar sequences. |
| digest(1e) | Reports on protein proteolytic enzyme or reagent cleavage sites. |
| distmat(1e) | Create a distance matrix from a multiple sequence alignment. |
| docxmlvalid(1e) | Check an XML document is well formed and conforms to a schema. |
| docxmlwell(1e) | Check an XML document is well formed. |
| domtesta(1e) | Reads an XML file into the DOM and writes it back out. |
| domtestb(1e) | Create, manipulate and write out XML. |
| domtestc(1e) | Create and write out some typical XML. |
| domtestd(1e) | Create some XML and search for an element. |
| dotmatcher(1e) | Draw a threshold dotplot of two sequences. |
| dottup(1e) | Displays a wordmatch dotplot of two sequences. |
| dreg(1e) | Regular expression search of nucleotide sequence(s). |
| drfinddata(1e) | Find public databases by data type. |
| drfindformat(1e) | Find public databases by format. |
| drfindid(1e) | Find public databases by identifier. |
| drfindresource(1e) | Find public databases by resource. |
| drget(1e) | Get data resource entries. |
| drtext(1e) | Get data resource entries complete text. |
| edamclean(1e) | Validate and fix EDAM OBO ontology. |
| edamdef(1e) | Find EDAM ontology terms by definition. |
| edamhasinput(1e) | Find EDAM ontology terms by has_input relation. |
| edamhasoutput(1e) | Find EDAM ontology terms by has_output relation. |
| edamisformat(1e) | Find EDAM ontology terms by is_format_of relation. |
| edamisid(1e) | Find EDAM ontology terms by is_identifier_of relation. |
| edamname(1e) | Find EDAM ontology terms by name. |
| edialign(1e) | Local multiple alignment of sequences. |
| einverted(1e) | Finds inverted repeats in nucleotide sequences. |
| em_cons(1e) ↣ cons(1e) | Create a consensus sequence from a multiple alignment. |
| em_pscan(1e) ↣ pscan(1e) | Scans protein sequence(s) with fingerprints from the PRINTS database. |
| embossdata(1e) | Find and retrieve EMBOSS data files. |
| embossversion(1e) | Reports the current EMBOSS version number. |
| emma(1e) | Multiple sequence alignment (ClustalW wrapper). |
| emowse(1e) | Search protein sequences by digest fragment molecular weight. |
| ensembltest(1e) | Demonstration of the Ensembl API to be. |
| entrails(1e) | Reports the internal data from the EMBOSS code. |
| entrailsbook(1e) | Reports the internal structures in EMBOSS book format. |
| entrailshtml(1e) | Reports the internal structures in HTML. |
| entrailswiki(1e) | Reports the internal structures in wikitext. |
| entret(1e) | Retrieves sequence entries from flatfile databases and files. |
| entrygo(1e) | Identify and retrieve sequence entries containing GO terms. |
| entrytax(1e) | Identify and retrieve sequence entries containing taxonomy IDs. |
| epestfind(1e) | Finds PEST motifs as potential proteolytic cleavage sites. |
| eprimer3(1e) | Picks PCR primers and hybridization oligos. |
| eprimer32(1e) | Picks PCR primers and hybridization oligos. |
| equicktandem(1e) | Finds tandem repeats in nucleotide sequences. |
| est2genome(1e) | Align EST sequences to genomic DNA sequence. |
| etandem(1e) | Finds tandem repeats in a nucleotide sequence. |
| extractalign(1e) | Extract regions from a sequence alignment. |
| extractfeat(1e) | Extract features from sequence(s). |
| extractseq(1e) | Extract regions from a sequence. |
| featcopy(1e) | Reads and writes a feature table. |
| featreport(1e) | Reads and writes a feature table. |
| feattext(1e) | Return a feature table original text. |
| findkm(1e) | Calculate and plot enzyme reaction data. |
| freak(1e) | Generate residue/base frequency table or plot. |
| fuzznuc(1e) | Search for patterns in nucleotide sequences. |
| fuzzpro(1e) | Search for patterns in protein sequences. |
| fuzztran(1e) | Search for patterns in protein sequences (translated). |
| garnier(1e) | Predicts protein secondary structure using GOR method. |
| geecee(1e) | Calculate fractional GC content of nucleic acid sequences. |
| getorf(1e) | Finds and extracts open reading frames (ORFs). |
| godef(1e) | Find GO ontology terms by definition. |
| goname(1e) | Find GO ontology terms by name. |
| goseq(1e) | Identify sequence entries containing GO terms. |
| helixturnhelix(1e) | Identify nucleic acid-binding motifs in protein sequences. |
| histogramtest(1e) | Test of graphics. |
| hmoment(1e) | Calculate and plot hydrophobic moment for protein sequence(s). |
| idtell(1e) | Identify the type of a data identifier or query term. |
| iep(1e) | Calculate the isoelectric point of proteins. |
| infoalign(1e) | Display basic information about a multiple sequence alignment. |
| infobase(1e) | Return information on a given nucleotide base. |
| inforesidue(1e) | Return information on a given amino acid residue. |
| infoseq(1e) | Display basic information about sequences. |
| intconv(1e) | Convert ints to ajints and longs to ajlongs. |
| isdbdata(1e) | Check whether a supplied string is a known data type/identifier name. |
| isdbname(1e) | Check whether a supplied string is a known database name. |
| isochore(1e) | Plots isochores in DNA sequences. |
| jaspextract(1e) | Extract data from JASPAR. |
| jaspscan(1e) | Scans DNA sequences for transcription factors. |
| lindna(1e) | Draws linear maps of DNA constructs. |
| listor(1e) | Write a list file of the logical OR of two sets of sequences. |
| makenucseq(1e) | Create random nucleotide sequences. |
| makeprotseq(1e) | Create random protein sequences. |
| marscan(1e) | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences. |
| martattributes(1e) | Return attributes from a mart dataset from a mart host. |
| martdatasets(1e) | Return datasets from a mart from a registry. |
| martfilters(1e) | Return filters from a mart dataset from a mart host. |
| martquery(1e) | Perform a biomart query. |
| martregistry(1e) | Show Biomart registries listed on a host. |
| martseqs(1e) | Show Biomart datasets that can return sequences. |
| maskambignuc(1e) | Masks all ambiguity characters in nucleotide sequences with N. |
| maskambigprot(1e) | Masks all ambiguity characters in protein sequences with X. |
| maskfeat(1e) | Write a sequence with masked features. |
| maskseq(1e) | Write a sequence with masked regions. |
| matcher(1e) | Waterman-Eggert local alignment of two sequences. |
| megamerger(1e) | Merge two large overlapping DNA sequences. |
| merger(1e) | Merge two overlapping sequences. |
| msbar(1e) | Mutate a sequence. |
| mwcontam(1e) | Find weights common to multiple molecular weights files. |
| mwfilter(1e) | Filter noisy data from molecular weights file. |
| needle(1e) | Needleman-Wunsch global alignment of two sequences. |
| needleall(1e) | Many-to-many pairwise alignments of two sequence sets. |
| newcoils(1e) | Predicts coils protein secondary structure. |
| newcpgreport(1e) | Identify CpG islands in nucleotide sequence(s). |
| newcpgseek(1e) | Identify and report CpG-rich regions in nucleotide sequence(s). |
| newseq(1e) | Create a sequence file from a typed-in sequence. |
| nohtml(1e) | Remove mark-up (e.g. HTML tags) from an ASCII text file. |
| noreturn(1e) | Remove carriage return from ASCII files. |
| nospace(1e) | Remove whitespace from an ASCII text file. |
| notab(1e) | Replace tabs with spaces in an ASCII text file. |
| notseq(1e) | Write to file a subset of an input stream of sequences. |
| nthseq(1e) | Write to file a single sequence from an input stream of sequences. |
| nthseqset(1e) | Reads and writes (returns) one set of sequences from many. |
| octanol(1e) | Draw a White-Wimley protein hydropathy plot. |
| oddcomp(1e) | Identify proteins with specified sequence word composition. |
| ontocount(1e) | Count ontology term(s). |
| ontoget(1e) | Get ontology term(s). |
| ontogetcommon(1e) | Get common ancestor for terms. |
| ontogetdown(1e) | Get ontology term(s) by parent id. |
| ontogetobsolete(1e) | Get ontology ontology terms. |
| ontogetroot(1e) | Get ontology root terms by child identifier. |
| ontogetsibs(1e) | Get ontology term(s) by id with common parent. |
| ontogetup(1e) | Get ontology term(s) by id of child. |
| ontoisobsolete(1e) | Report whether an ontology term id is obsolete. |
| ontotext(1e) | Get ontology term(s) original full text. |
| origsplitter(1e) | Split a sequence into (overlapping) smaller sequences. |
| origunion(1e) | Reads sequence fragments and builds one sequence. |
| palindrome(1e) | Finds inverted repeats in nucleotide sequence(s). |
| pasteseq(1e) | Insert one sequence into another. |
| patmatdb(1e) | Searches protein sequences with a sequence motif. |
| patmatmotifs(1e) | Scan a protein sequence with motifs from the PROSITE database. |
| patmattest(1e) | Test of pattern matching. |
| pepcoil(1e) | Predicts coiled coil regions in protein sequences. |
| pepdigest(1e) | Reports on protein proteolytic enzyme or reagent cleavage sites. |
| pepinfo(1e) | Plot amino acid properties of a protein sequence in parallel. |
| pepnet(1e) | Draw a helical net for a protein sequence. |
| pepstats(1e) | Calculates statistics of protein properties. |
| pepwheel(1e) | Draw a helical wheel diagram for a protein sequence. |
| pepwindow(1e) | Draw a hydropathy plot for a protein sequence. |
| pepwindowall(1e) | Draw Kyte-Doolittle hydropathy plot for a protein alignment. |
| plotcon(1e) | Plot conservation of a sequence alignment. |
| plotorf(1e) | Plot potential open reading frames in a nucleotide sequence. |
| polydot(1e) | Draw dotplots for all-against-all comparison of a sequence set. |
| preg(1e) | Regular expression search of protein sequence(s). |
| prettyplot(1e) | Draw a sequence alignment with pretty formatting. |
| prettyseq(1e) | Write a nucleotide sequence and its translation to file. |
| prima(1e) | Selects primers for PCR and DNA amplification. |
| primers(1e) | Simple version of primer3 to pick PCR primers. |
| primersearch(1e) | Search DNA sequences for matches with primer pairs. |
| printsextract(1e) | Extract data from PRINTS database for use by pscan. |
| profit(1e) | Scan one or more sequences with a simple frequency matrix. |
| prophecy(1e) | Create frequency matrix or profile from a multiple alignment. |
| prophet(1e) | Scan one or more sequences with a Gribskov or Henikoff profile. |
| prosextract(1e) | Processes the PROSITE motif database for use by patmatmotifs. |
| pscan(1e) | Scans protein sequence(s) with fingerprints from the PRINTS database. |
| psiphi(1e) | Calculates phi and psi torsion angles from protein coordinates. |
| rebaseextract(1e) | Process the REBASE database for use by restriction enzyme applications. |
| recoder(1e) | Find restriction sites to remove (mutate) with no translation change. |
| redata(1e) | Retrieve information from REBASE restriction enzyme database. |
| remap(1e) | Display restriction enzyme binding sites in a nucleotide sequence. |
| restover(1e) | Find restriction enzymes producing a specific overhang. |
| restrict(1e) | Report restriction enzyme cleavage sites in a nucleotide sequence. |
| revseq(1e) | Reverse and complement a nucleotide sequence. |
| seealso(1e) | Finds programs with similar function to a specified program. |
| seqcount(1e) | Reads and counts sequences. |
| seqgo(1e) | Extract a list of GO terms from a sequence entry. |
| seqinfo(1e) | Returns sequence information. |
| seqmatchall(1e) | All-against-all word comparison of a sequence set. |
| seqret(1e) | Reads and writes (returns) sequences. |
| seqretall(1e) | Reads and writes (returns) a set of sequences one at a time. |
| seqretallfeat(1e) | Reads and writes (returns) one or more sequences. |
| seqretset(1e) | Reads and writes (returns) a set of sequences all at once. |
| seqretsetall(1e) | Reads and writes (returns) many sets of sequences. |
| seqretsingle(1e) | Reads and writes (returns) a single sequence. |
| seqretsplit(1e) | Reads sequences and writes them to individual files. |
| seqrettype(1e) | Reads and writes (returns) sequences. |
| seqtax(1e) | Extract a list of taxonomy ids from a sequence entry. |
| seqxref(1e) | Retrieve all database cross-references for a sequence entry. |
| seqxrefall(1e) | Retrieve all cross-references for a sequence record. |
| seqxrefget(1e) | Retrieve all cross-referenced data for a sequence entry. |
| servertell(1e) | Display information about a public server. |
| showalign(1e) | Display a multiple sequence alignment in pretty format. |
| showdb(1e) | Displays information on configured databases. |
| showfeat(1e) | Display features of a sequence in pretty format. |
| showorf(1e) | Display a nucleotide sequence and translation in pretty format. |
| showpep(1e) | Displays protein sequences with features in pretty format. |
| showseq(1e) | Displays sequences with features in pretty format. |
| showserver(1e) | Displays information on configured servers. |
| shuffleseq(1e) | Shuffles a set of sequences maintaining composition. |
| sigcleave(1e) | Reports on signal cleavage sites in a protein sequence. |
| silent(1e) | Find restriction sites to insert (mutate) with no translation change. |
| sirna(1e) | Finds siRNA duplexes in mRNA. |
| sixpack(1e) | Display a DNA sequence with 6-frame translation and ORFs. |
| sizeseq(1e) | Sort sequences by size. |
| skipredundant(1e) | Remove redundant sequences from an input set. |
| skipseq(1e) | Reads and writes (returns) sequences, skipping first few. |
| splitsource(1e) | Split sequence(s) into original source sequences. |
| splitter(1e) | Split sequence(s) into smaller sequences. |
| sqltest(1e) | Demonstration of SQL server access. |
| stretcher(1e) | Needleman-Wunsch rapid global alignment of two sequences. |
| stssearch(1e) | Search a DNA database for matches with a set of STS primers. |
| supermatcher(1e) | Calculate approximate local pair-wise alignments of larger sequences. |
| syco(1e) | Draw synonymous codon usage statistic plot for a nucleotide sequence. |
| taxget(1e) | Get taxon(s). |
| taxgetdown(1e) | Get descendants of taxon(s). |
| taxgetrank(1e) | Get parents of taxon(s). |
| taxgetspecies(1e) | Get all species under taxon(s). |
| taxgetup(1e) | Get parents of taxon(s). |
| taxseq(1e) | Identify sequence entries containing taxonomy IDs. |
| tcode(1e) | Identify protein-coding regions using Fickett TESTCODE statistic. |
| testplot(1e) | Test plot. |
| textget(1e) | Get text data entries. |
| textsearch(1e) | Search the textual description of sequence(s). |
| texttotext(1e) | Convert a plain text format to a different format. |
| texttoxml(1e) | Convert a plain text format to an XML format. |
| textvalid(1e) | Check a plain text format is valid. |
| tfextract(1e) | Process TRANSFAC transcription factor database for use by tfscan. |
| tfm(1e) | Displays full documentation for an application. |
| tfscan(1e) | Identify transcription factor binding sites in DNA sequences. |
| tmap(1e) | Predict and plot transmembrane segments in protein sequences. |
| tranalign(1e) | Generate an alignment of nucleic coding regions from aligned proteins. |
| transeq(1e) | Translate nucleic acid sequences. |
| treetypedisplay(1e) | Test of graphics. |
| trimest(1e) | Remove poly-A tails from nucleotide sequences. |
| trimseq(1e) | Remove unwanted characters from start and end of sequence(s). |
| trimspace(1e) | Remove extra whitespace from an ASCII text file. |
| twofeat(1e) | Finds neighbouring pairs of features in sequence(s). |
| union(1e) | Concatenate multiple sequences into a single sequence. |
| urlget(1e) | Get URLs of data resources. |
| vectorstrip(1e) | Removes vectors from the ends of nucleotide sequence(s). |
| water(1e) | Smith-Waterman local alignment of sequences. |
| whichdb(1e) | Search all sequence databases for an entry and retrieve it. |
| wobble(1e) | Plot third base position variability in a nucleotide sequence. |
| wordcount(1e) | Count and extract unique words in molecular sequence(s). |
| wordfinder(1e) | Match large sequences against one or more other sequences. |
| wordmatch(1e) | Finds regions of identity (exact matches) of two sequences. |
| wossdata(1e) | Finds programs by EDAM data. |
| wossinput(1e) | Finds programs by EDAM input data. |
| wossname(1e) | Finds programs by keywords in their short description. |
| wossoperation(1e) | Finds programs by EDAM operation. |
| wossoutput(1e) | Finds programs by EDAM output data. |
| wossparam(1e) | Finds programs by EDAM parameter. |
| wosstopic(1e) | Finds programs by EDAM topic. |
| xmltotext(1e) | Convert an XML document to a plain text format. |
| xmltoxml(1e) | Convert an XML document to a different format. |
| xmltransform(1e) | Convert an XML document to a different format using a supplied XSLT file. |
| yank(1e) | Add a sequence reference (a full USA) to a list file. |