section 1e — User commands

• 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
• allversusall(1e) Sequence similarity data from all-versus-all comparison.
• 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
• cathparse(1e) Generates DCF file from raw CATH files.
• 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
• domainalign(1e) Generate alignments (DAF file) for nodes in a DCF file.
• domainnr(1e) Removes redundant domains from a DCF file.
• domainrep(1e) Reorder DCF file to identify representative structures.
• domainreso(1e) Remove low resolution domains from a DCF file.
• domainseqs(1e) Adds sequence records to a DCF file.
• domainsse(1e) Add secondary structure records to a DCF file.
• 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
• dotpath(1e) Draw a non-overlapping wordmatch 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
• 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
• libscan(1e) Diagnostic searches for protein families.
• libscanout(1e) Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies.
• 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
• scopparse(1e) Generate DCF file from raw SCOP files.
• seealso(1e) Finds programs with similar function to a specified program
• seqalign(1e) Extend alignments (DAF file) with sequences (DHF file).
• seqcount(1e) Reads and counts sequences
• seqfraggle(1e) Removes fragment sequences from DHF files.
• 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
• seqnr(1e) Removes redundancy from DHF files.
• 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
• seqsearch(1e) Generate PSI-BLAST hits (DHF file) from a DAF file.
• seqsort(1e) Remove ambiguous classified sequences from DHF files.
• seqtax(1e) Extract a list of taxonomy ids from a sequence entry
• seqwords(1e) Generates DHF files from keyword search of UniProt.
• 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
• ssematch(1e) Search a DCF file for secondary structure matches.
• 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