www_pcm_uam_es.pm - Library for www_pcm_uam_es services.
Usage:
my $obj = Object->new ('src_human','Uniprot');
print $obj->toString;
my $aaSeq = inb_bsc_es::getAminoAcidSequence(
'input' => $obj
) -> {'sequence'};
print $aaSeq->SequenceString;
refreshWSDL parameter:
All methods have an additional parameter 'refreshWSDL' used to refresh the service WSDL. Default value is "false".
my $aaSeq = inb_bsc_es::getAminoAcidSequence(
'input' => $obj,
'refreshWSDL' => "true"
) -> {'sequence'};
See also runService.
Library to run available services from www_pcm_uam_es.
Converts a collection of amino acid sequences into a FASTA_pep.
(modified_FASTA_format => FASTA_pep) = fromAASeqCollectionToFastaPep ( sequences => [AminoAcidSequence] )
Converts an alignment in Clustalw format into Phylip format.
(phylip_alignment => Phylip_Interleaved_Text) = fromClustalwToPhylip ( clustalw_alignment => Clustalw_Text )
Converts a sequence in Fasta format into an AminoAcidSequence object.
(aminoacid => AminoAcidSequence) = fromFastaToAminoAcidSequence ( fasta => FASTA )
Converts a sequence in Fasta format into a CommentedAASequence object.
(aminoacid => CommentedAASequence) = fromFastaToCommentedAASequence ( fasta => FASTA )
Converts a sequence in Fasta format into a CommentedNASequence object.
(nucleotide => CommentedNASequence) = fromFastaToCommentedNASequence ( fasta => FASTA )
Converts a sequence in Fasta format into a GenericSequence object.
(sequence => GenericSequence) = fromFastaToGenericSequence ( fasta => FASTA )
Converts a sequence in Fasta format into a NucleotideSequence object.
(nucleotide => NucleotideSequence) = fromFastaToNucleotideSequence ( fasta => FASTA )
Converts a GenericSequence object into an AminoAcidSequence.
(aminoacid => AminoAcidSequence) = fromGenericToAminoAcidSequence ( sequence => GenericSequence )
Converts a GenericSequence object into a NucleotideSequence.
(nucleotide => GenericSequence) = fromGenericToNucleotideSequence ( sequence => GenericSequence )
Runs DSSP program to extract the secondary structure from the PDB input.
(result => DSSP_Text) = fromPDBTextToDSSP ( pdbEntry => PDB__Text )
Retrieves an aminoacid sequence from an aminoacid database.
(sequence => AminoAcidSequence) = getAminoAcidSequence ( id => Object )
Extracts CATH domain names from PDB ID.
(CATH_domain_names => [Object]) = getCATHDomainNamesFromPDBID ( PDBID => Object )
Extract CDS sequences.
(sequences => [NucleotideSequence]) = getCDSSequence ( input => Object )
This is a utility to extract the Codon Usage Tables used by EMBOSS programs.
(codon_usage_table => CodonUsageTable_Text) = getCodonTableFromEmboss ( table_name => Object )
Retrieves a documentation file from Prosite.
(prosite_doc => PrositeDoc_Text) = getDocumentationFromProsite ( id => Object )
Extracts domain definitions from CATH.
(cath_doc => CathDomainDescription_XML) = getDomainDescriptionFromCATH ( CathDomainID => Object )
Retrieves an entry from DSSP database.
(entry => DSSP_Text) = getEntryFromDSSP ( id => Object )
Retrieves an entry from EMBL database.
(entry => EMBL_Text) = getEntryFromEMBL ( id => Object )
Retrieves an entry from FSSP database.
(entry => FSSP_Text) = getEntryFromFSSP ( id => Object )
Retrieves an entry from GenBank database.
(entry => GenBank_Text) = getEntryFromGenBank ( id => Object )
Retrieves an entry from HSSP database.
(entry => HSSP_Text) = getEntryFromHSSP ( id => Object )
Retrieves structures (whole PDB entries or single chains) from PDB database in PDB format.
(entry => PDB__Text) = getEntryFromPDB ( id => Object )
Provides a full PDB entry in mmCIF format.
(entry => mmCIF_Text) = getEntryFromPDBmmCIF ( id => Object )
Retrieves an entry from Pfam database.
(entry => HMM_Text) = getEntryFromPfam ( id => Object )
Retrieves an entry from RefSeq database.
(entry => RefSeq_Text) = getEntryFromRefSeq ( id => Object )
Retrieves an entry from Swiss-Prot database.
(entry => SwissProt_Text) = getEntryFromSwissProt ( id => Object )
Retrieves an entry from TrEMBL database.
(entry => SwissProt_Text) = getEntryFromTrEMBL ( id => Object )
Retrieves an entry from UniProt database.
(entry => SwissProt_Text) = getEntryFromUniProt ( id => Object )
Retrieves a sequence in Fasta format from a database.
(sequence => FASTA) = getFastaSequence ( id => Object )
Retrieves a nucleotide sequence from a nucleotide database.
(sequence => NucleotideSequence) = getNucleotideSequence ( id => Object )
Extracts hits from a blast report.
(hits => [Object]) = parseBlastReportIntoHits ( blast_report => BLAST__Text )
Parses a PDB entry into its corresponding sequences.
(sequence_chains => [GenericSequence]) = parsePDBIntoSeqs ( entry => Object )
Extracts PDB ids from a Swiss-Prot entry.
(ids => [Object]) = parseSwissIntoPDBids ( swiss_entry => SwissProt_Text )
Makes a ClustalW multiple sequence alignment (fast method).
(alignment => Clustalw_Text) = runClustalwFast ( sequences => [GenericSequence], matrix => String, pairgap => Integer, endgaps => String, topdiag => Integer, window => Integer, transitions_weight => Float, gapdist => Integer, gapext => Float, ktup => Integer, gapopen => Float )
Makes a ClustalW multiple sequence alignment (full method).
(alignment => Clustalw_Text) = runClustalwFull ( sequences => [GenericSequence], gapext => Float, transitions_weight => Float, pwmatrix => String, matrix => String, endgaps => String, gapdist => Integer, pwgapext => Float, gapopen => Float, pwgapopen => Float )
Analyzes protein sequences to find possible GPI-anchor sites.
(dgpi_protein => DGPI_Report) = runDGPIFromSequence ( sequence => GenericSequence )
Makes a pairwise structure comparison between two PDB chains.
(dalilite_report => Structure_Alignment_Report) = runDaliLite ( entry1 => PDB__Text, entry2 => PDB__Text )
Performs one-against-all pairwise alignments using 3D lookup and exhaustive search (Parsi method), or Soap if the query structure has few secondary structure elements.
(dccp_report => DCCP_Text) = runDaliLiteAgainstPDB ( id => Object )
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.
(antigenic_report => AntigenicReport) = runEmbossAntigenicFromID ( usa => Object, to => Integer, from => Integer, minlen => Integer )
Reads a protein sequence and calculates the charges of the amino acids within a window of specified length.
(charge_report => FeatureAASequence) = runEmbossChargeFromID ( usa => Object, to => Integer, window => Integer, from => Integer )
Compares two codon usage tables.
(codcmp_report => CodcmpReport_Text) = runEmbossCodcmpFromTables ( codon1 => CodonUsageTable_Text, codon2 => CodonUsageTable_Text )
Creates a consensus from multiple alignments.
(consensus_sequence => Consensus_Sequence_Text) = runEmbossConsFromAlignment ( alignment => Sequence_alignment_report, identity => Integer, plurality => Integer, setcase => Integer, matrix => String )
reads a collection of computer-readable trees and prints out a consensus tree.
(phylogenetic_tree => Newick_Text) = runEmbossConsense ( phylogenetic => [Newick_Text], root => Integer, outgroup_root => String, outgnum => Integer )
Plots CpG rich areas.
(CpGplot => Image_Encoded) = runEmbossCpGplotFromID ( usa => Object, to => Integer, window => Integer, from => Integer, minpc => Float, minoe => Float, minlen => Float )
Scans a nucletide sequence for higher than expected frequencies of the dinucleotide CG.
(CpG => CpGReport) = runEmbossCpGreportFromID ( usa => Object, to => Integer, from => Integer, score => Integer )
Reads a CDS sequence and calculates a codon frequency table.
(cusp_report => CodonUsageTable_Text) = runEmbossCuspFromID ( usa => Object, to => Integer, from => Integer )
Search a protein database for matches with the mass spectrometry data.
(identified_peptides => [EmowseAnnotatedAASequence]) = runEmbossEmowse ( mol_weights => ArrayFloat, database => String, pcrange => Integer, partials => Float, weight => Integer, tolerance => Float, enzyme => String )
Scans a sequence for potential tandem repeats.
(repeats => EquicktandemReport) = runEmbossEquicktandemFromID ( usa => Object, to => Integer, threshold => Integer, from => Integer, maxrepeat => Integer )
Finds the Michaelis Menten constant (Km) and the maximum velocity (Vmax) for an enzyme reaction by a Michaelis Menten and Hanes/Woolf plot.
(KmVmaxplot => Image_Encoded) = runEmbossFindkm ( kinetics => Enzymatic_Text )
Finds and extracts open reading frames (ORFs).
(open_reading_frames => [CommentedAASequence]) = runEmbossGetorfFromID ( id => Object, minsize => Integer, circular => String, table => Integer, methionine => String, maxsize => Integer, find => Integer, reverse => String, to => Integer, flanking => Integer, from => Integer )
Makes a pairwise global alignment using the Needleman-Wunsch algorithm.
(pairwise_alignment => MSF) = runEmbossNeedleFromIDs ( usa_1 => Object, usa_2 => Object, gapextend => Float, datafile => String, gapopen => Float )
Displays protein hydropathy.
(octanol_report => Image_Encoded) = runEmbossOctanolFromID ( usa => Object, width => Integer, differenceplot => String, to => Integer, octanolplot => String, from => Integer, interfaceplot => String )
Takes a protein motif and compares it to a protein sequence.
(patmatdb_report => PatmatdbReport) = runEmbossPatmatdbFromID ( usa => Object, pattern => Pattern, to => Integer, from => Integer )
Takes a protein sequence and compares it to the PROSITE database.
(patmatmotifs_report => PatmatmotifsReport) = runEmbossPatmatmotifsFromID ( usa => Object, prune => String, to => Integer, from => Integer )
Coiled coil region prediction.
(coil_prediction => Pepcoil_Text) = runEmbossPepcoilFromID ( usa => Object, to => Integer, from => Integer )
Detects and displays various metrics about a protein sequence.
(pepinfo_report => PepinfoReport) = runEmbossPepinfoFromID ( usa => Object, hwindow => Integer, to => Integer, from => Integer )
Outputs a report of simple protein sequence information.
(protein_statistics => Pepstats_Text) = runEmbossPepstatsFromID ( usa => Object, to => Integer, from => Integer )
Produces a graph of the classic Kyte and Doolittle hydropathy plot of a protein.
(pepwindow_report => Image_Encoded) = runEmbossPepwindowFromID ( usa => Object, length => Integer, to => Integer, from => Integer )
Produces a set of superimposed Kyte and Doolittle hydropathy plots from an aligned set of protein sequences.
(pepwindowall_report => Image_Encoded) = runEmbossPepwindowallFromSequences ( sequences => Sequence_alignment_report, length => Integer )
Scans a nucletide sequence for restriction enzyme cleavage sites.
(restriction_cleavage_site => RestrictReport) = runEmbossRestrictFromID ( usa => Object, min => Integer, commercial => String, enzymes => String, max => Integer, ambiguity => String, single => String, to => Integer, blunt => String, sticky => String, from => Integer, sitelen => Integer, plasmid => String, limit => String )
Predicts the site of cleavage between a signal sequence and the mature exported protein.
(signal_peptides => SigcleaveReport) = runEmbossSigcleaveFromID ( usa => Object, to => Integer, from => Integer, minweight => Float )
Scans DNA sequences for transcription factors.
(TF_prediction => TFscan_Text) = runEmbossTFscanFromID ( usa => Object, to => Integer, mismatch => Integer, from => Integer, menu => String )
Displays membrane spanning regions.
(transmembrane_prediction => TransmembraneReport) = runEmbossTmapSequenceFromID ( usa => Object, to => Integer, from => Integer )
Translates nucleic acid sequences to the corresponding peptide sequence.
(translated_seq => CommentedAASequence) = runEmbossTranseqFromID ( usa => Object, to => Integer, trim => String, from => Integer, table => Integer, alternative => String, frame => String, clean => String )
Makes a pairwise local alignment using the Smith-Waterman algorithm.
(pairwise_alignment => MSF) = runEmbossWaterFromIDs ( usa_1 => Object, usa_2 => Object, gapextend => Float, datafile => String, gapopen => Float )
Creates the PDB files from the CATH domains especifications.
(PDB_domains => [PDB__Text]) = runExtractCATHdomainsFromID ( domainID => [Object] )
Compares a protein sequence against a protein database using the FASTA algorithm.
(fasta_report => FASTA_Text) = runFastaForAminoAcids ( sequence => AminoAcidSequence, database => String, expectation_upper_value => Float, ktup => Integer, gap_extension => Integer, high_scores_number => Integer, alignments_number => Integer, gap_open => Integer, scoring_matrix => String )
Compares a nucleic acid sequence against a nucleic acid database using the FASTA algorithm.
(fasta_report => FASTA_Text) = runFastaForNucleotides ( sequence => NucleotideSequence, ktup => Integer, database => String, expectation_upper_value => Float, gap_extension => Integer, high_scores_number => Integer, alignments_number => Integer, gap_open => Integer )
Compares an ordered peptide mixture, as would be obtained by Edman degradation of a CNBr cleavage of a protein, againts a peptide database.
(fasta_report => FASTA_Text) = runFastf ( sequence => [AminoAcidSequence], ktup => Integer, database => String, high_scores_number => Integer, alignments_number => Integer, scoring_matrix => String )
Compares short peptide fragments, as would be obtained from mass-spec. analysis of a protein, against a protein database.
(fasta_report => FASTA_Text) = runFasts ( sequence => [AminoAcidSequence], ktup => Integer, database => String, high_scores_number => Integer, alignments_number => Integer, scoring_matrix => String )
Constructs a Hidden Markov Model from a multiple sequence alignment.
(profile => HMM_Text) = runHMMBuild ( alignment => Sequence_alignment_report, swentry => Float, fast_algorithm => String, architecture_prior => Float, weighting_algorithm => String, fast_construction => Float, idlevel => Float, pb_weights => Integer, alignment_method => String, swexit => Float )
Searches a HMM profile database (Pfam) with a query sequence.
(hmmpfam_report => HMMPfam_Report) = runHMMPfam ( sequence => AminoAcidSequence, e__value_score => Integer, score_cutoff => Float, alignment_number => Integer, e__value_domain => Float, hmm_accesions => String, score_cutoff_domain => Float, e__value => Float )
Searches a sequence database with a HMM profile.
(hmmsearch_report => HMMSearch_Report) = runHMMSearchAgainstDB ( profile => HMM_Text, database => String, e__value_domain => Float, alignment_number => Integer, score_cutoff => Float, e__value_score => Integer, score_cutoff_domain => Float, e__value => Float )
Searches a set of sequences with a HMM profile.
(hmmsearch_report => HMMSearch_Report) = runHMMSearchAgainstSeqs ( profile => HMM_Text, sequences => [GenericSequence], e__value => Float, score_cutoff_domain => Float, e__value_score => Integer, score_cutoff => Float, alignment_number => Integer, e__value_domain => Float )
Infers the novo peptides from mass spectra using Lutefisk.
(denovo_peptides => LutefiskReport) = runLutefiskFromDTA ( dta => DTA_Text )
Compares a nucleotide sequence to a sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastn ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, database => String, gapalign => String, opengap => Integer )
Compares a nucleotide sequence to a sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). Returns a XML report.
(blast_report => BLAST_XML) = runNCBIBlastnXML ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, database => String, gapalign => String, opengap => Integer )
Compares a nucleotide sequence against another nucleotide sequence using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastn_2Seqs ( sequence_1 => NucleotideSequence, sequence_2 => NucleotideSequence, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, match => Integer, mismatch => Integer, gapalign => String, opengap => Integer )
Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastp ( sequence => AminoAcidSequence, matrix => String, alignments => Integer, extendgap => Integer, filter => String, expected_threshold => Float, dropoff => Integer, scores => Integer, database => String, gapalign => String, opengap => Integer )
Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). Returns a XML report.
(blast_report => BLAST_XML) = runNCBIBlastpXML ( sequence => AminoAcidSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a protein sequence against another protein sequence using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastp_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => AminoAcidSequence, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Compares a nucleotide sequence to a protein sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastx ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a nucleotide sequence to a protein sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). Returns a XML report.
(blast_report => BLAST_XML) = runNCBIBlastxXML ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a nucleotide query sequence translated in all reading frames against a protein sequence using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastx_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => NucleotideSequence, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Compares a protein sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastn ( sequence => AminoAcidSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a protein sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). Returns a XML report.
(blast_report => BLAST_XML) = runNCBITBlastnXML ( sequence => AminoAcidSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a protein sequence against a nucleotide sequence dynamically translated in all six reading frames (both strands) using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastn_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => NucleotideSequence, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Compares a nucleotide sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastx ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares a nucleotide sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). Returns a XML report.
(blast_report => BLAST_XML) = runNCBITBlastxXML ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, gapalign => String, opengap => Integer )
Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastx_2Seqs ( sequence_1 => NucleotideSequence, sequence_2 => NucleotideSequence, dropoff => Integer, expected_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database.
(ppsearch_report => PPSearchReport) = runPPSearchAgainstProsite ( sequence => AminoAcidSequence, abundantPatterns => String )
Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Position Specific Iterative BLAST (PSI-BLAST) and returns a blast report.
(blast_report => BLAST__Text) = runPSIBlast ( sequence => AminoAcidSequence, scores => Integer, filter => String, extendgap => Integer, alignments => Integer, nrounds => Integer, constant => Integer, matrix => String, database => String, mexpect => Float, gapalign => String, wordsize => Integer, expect => Float, opengap => Integer )
Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Position Specific Iterative BLAST (PSI-BLAST) and returns a blast report. Returns a XML report.
(blast_report => BLAST_XML) = runPSIBlastXML ( sequence => AminoAcidSequence, scores => Integer, filter => String, extendgap => Integer, alignments => Integer, nrounds => Integer, constant => Integer, matrix => String, database => String, mexpect => Float, gapalign => String, wordsize => Integer, expect => Float, opengap => Integer )
Infers the novo peptides from mass spectra using PepNovo.
(denovo_peptides => [PepNovoReport]) = runPepNovoFromDTA ( dta => [DTA_Text] )
Uses nucleotide sequences to compute a distance matrix, under four different models of nucleotide substitution.
(matrix => Distance_Matrix) = runPhylipDnadist ( alignment => Phylip_Text, ttratio => Float, method => String, basefrequency => String, freqt => Float, matrix => String, freqc => Float, freqg => Float, freqa => Float )
Estimates phylogenies from nucleotide sequences by maximum likelihood.
(phylogenetic_tree => Newick_Text) = runPhylipDnaml ( alignment => Phylip_Text, outgnum => Integer, ttratio => Integer, random => String, basefrequency => String, outgroup_root => String, freqt => Float, randtimes => Integer, freqc => Float, lambda => Float, global => String, freqg => Float, freqa => Float, randseed => Integer )
Estimates phylogenies from nucleotide sequences by maximum likelihood under the constraint that the trees estimated must be consistent with a molecular clock.
(phylogenetic_tree => Newick_Text) = runPhylipDnamlk ( alignment => Phylip_Text, global => String, freqg => Float, freqa => Float, randseed => Integer, lambda => Float, freqc => Float, randtimes => Integer, freqt => Float, basefrequency => String, random => String, ttratio => Integer )
Estimates phylogenies from nucleotide sequences by unrooted parsimony.
(phylogenetic_tree => Newick_Text) = runPhylipDnapars ( alignment => Phylip_Text, outgnum => Integer, outgroup_root => String, randtimes => Integer, threshold => Float, randseed => Integer, random => String )
Estimates phylogenies from nucleotide sequences by branch and bound method.
(phylogenetic_tree => Newick_Text) = runPhylipDnapenny ( alignment => Phylip_Text, theshold => Float, numgroups => Integer, howoften => Integer, simple => String, outgroup_root => String, outgnum => Integer )
Estimates phylogenies from distance matrix data using the Fitch-Margoliash method and some related least squares methods.
(phylogenetic_tree => Newick_Text) = runPhylipFitch ( matrix => Distance_Matrix, randseed => Integer, global => String, negativebranch => String, randtimes => Integer, matrix => String, outgroup_root => String, random => String, power => Integer, subreplicates => String, outgnum => Integer )
Carries out the Fitch-Margoliash and Least-Squares methods, plus a variety of others of the same family, with the assumption that all tip species are contemporaneous, and there is an evolutionary clock.
(phylogenetic_tree => Newick_Text) = runPhylipKitsch ( matrix => Distance_Matrix, matrix => String, randtimes => Integer, negativebranch => String, randseed => Integer, random => String, subreplicates => String )
Estimates phylogenies from distance matrix data using the Neighbor-Joining method or the UPGMA method of clustering.
(phylogenetic_tree => Newick_Text) = runPhylipNeighbor ( matrix => Distance_Matrix, subreplicates => String, matrix => String, method => String, randseed => Integer, random => String, outgroup_root => String, outgnum => Integer )
Uses protein sequences to compute a distance matrix, under three different models of aminoacid replacement.
(matrix => Distance_Matrix) = runPhylipProtdist ( alignment => Phylip_Text, gencode => String, ttratio => Float, category => String, changeprob => Float, method => String )
Estimates phylogenies from protein sequences by unrooted parsimony.
(phylogenetic_tree => Newick_Text) = runPhylipProtpars ( alignment => Phylip_Text, random => String, randseed => Integer, threshold => Float, randtimes => Integer, outgroup_root => String, outgnum => Integer )
Search for patterns conserved in a set of protein sequences.
(pratt_report => [MatchingPattern]) = runPratt ( sequence => [AminoAcidSequence], maxWildcards => Integer, refinement => String, greedines => Integer, generalise => String, maxNumPatterns => Integer, maxLength => Integer, maxSymbols => Integer, minNumSeqs => Integer, maxFlexibleWildcards => Integer )
Scans a protein sequence for the occurence of patterns and profiles stored in the PROSITE database.
(ps_scan_report => MotifAnnotatedAASequence) = runPs_scanAgainstProsite ( sequence => AminoAcidSequence, cutoff => Integer, skipProfiles => String, skipFrequent => String )
Scans a protein sequence for the occurrence of a pattern.
(ps_scan_report => MotifAnnotatedAASequence) = runPs_scanAgainstSequence ( pattern => Pattern, sequence => AminoAcidSequence, maximumMatches => Integer, included => String, greediness => String, overlap => String )
Evaluation of an alignment using Tcoffee.
(tcoffee_evaluation => Clustalw_Evaluated_Text) = runTcoffeeEvaluateAlignments ( alignment => Clustalw_Text )
Makes a profile alignment using Tcoffee.
(tcoffee_report => Clustalw_Text) = runTcoffeeFromProfiles ( alignments => [Clustalw_Text], profile_mode => String, clustalw_header => String, profile_comparison => String )
Makes a multiple sequence alignment using Tcoffee.
(tcoffee_report => Clustalw_Text) = runTcoffeeFromSequences ( sequences => [GenericSequence], method => String, tree_mode => String, do_normalise => Integer, dp_mode => String, clustalw_header => String, ktuple => Integer, extend_mode => String, diag_mode => Integer, gapext => Integer, extend => Integer, ndiag => Integer, gapopen => Integer )
It compares a nucleotide query sequence against a nucleotide sequence database using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastn ( sequence => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, match => Integer, alignments => Integer, database => String, mismatch => Integer, nogaps => String, gap_open => Integer )
Compares a nucleotide query sequence against another nucleotide sequence using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastn_2Seqs ( sequence_1 => NucleotideSequence, sequence_2 => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, match => Integer, alignments => Integer, mismatch => Integer, nogaps => String, gap_open => Integer )
It compares an amino acid query sequence against a protein sequence database using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastp ( sequence => AminoAcidSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, database => String, nogaps => String, gap_open => Integer )
Compares a protein sequence against another protein sequence using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastp_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => AminoAcidSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, alignments => Integer, matrix => String, nogaps => String, gap_open => Integer )
It compares a nucleotide query sequence against a protein sequence database using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastx ( sequence => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, database => String, nogaps => String, gap_open => Integer )
Compares a nucleotide query sequence translated in all reading frames against a protein sequence using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUBlastx_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, nogaps => String, gap_open => Integer )
It compares an amino acid query sequence against the six-frame translations of a nucleotide sequence database using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUTBlastn ( sequence => AminoAcidSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, database => String, nogaps => String, gap_open => Integer )
Compares a protein sequence against a nucleotide sequence dynamically translated in all six reading frames using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUTBlastn_2Seqs ( sequence_1 => AminoAcidSequence, sequence_2 => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, nogaps => String, gap_open => Integer )
It compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUTBlastx ( sequence => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, database => String, nogaps => String, gap_open => Integer )
Compares a nucleotide query sequence against another nucleotide sequence using the Washington University BLAST algorithm.
(wublast_report => BLAST__Text) = runWUTBlastx_2Seqs ( sequence_1 => NucleotideSequence, sequence_2 => NucleotideSequence, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, nogaps => String, gap_open => Integer )
Queries an Amino Acid sequence against InterPro.
(iprscan_report => InterProMotifAnnotatedAASequence) = searchInterPro ( sequence => AminoAcidSequence, blastprodom => String, hmmpfam => String, hmmtigr => String, profilescan => String, hmmpanther => String, scanregexp => String, gene3d => String, coils => String, superfamily => String, hmmpir => String, seg => String, fprintscan => String, hmmsmart => String )
Searches entries from UniProt containing a specified keyword in one of the chosen fields.
(description => [SequenceDescription_Text]) = searchKeywordInUniProt ( content => String, field => String )