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Carta.tech
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Packages
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emboss
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318
- 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
- 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
- em_cons.1e
- Create a consensus sequence from a multiple alignment
- em_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