NAME

www_pcm_uam_es.pm - Library for www_pcm_uam_es services.

SYNOPSIS

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.

DESCRIPTION

Library to run available services from www_pcm_uam_es.

METHODS

fromAASeqCollectionToFastaPep

Converts a collection of amino acid sequences into a FASTA_pep.

 (modified_FASTA_format => FASTA_pep) = fromAASeqCollectionToFastaPep 
		(
			sequences => [AminoAcidSequence]
		)

fromClustalwToPhylip

Converts an alignment in Clustalw format into Phylip format.

 (phylip_alignment => Phylip_Interleaved_Text) = fromClustalwToPhylip 
		(
			clustalw_alignment => Clustalw_Text
		)

fromFastaToAminoAcidSequence

Converts a sequence in Fasta format into an AminoAcidSequence object.

 (aminoacid => AminoAcidSequence) = fromFastaToAminoAcidSequence 
		(
			fasta => FASTA
		)

fromFastaToCommentedAASequence

Converts a sequence in Fasta format into a CommentedAASequence object.

 (aminoacid => CommentedAASequence) = fromFastaToCommentedAASequence 
		(
			fasta => FASTA
		)

fromFastaToCommentedNASequence

Converts a sequence in Fasta format into a CommentedNASequence object.

 (nucleotide => CommentedNASequence) = fromFastaToCommentedNASequence 
		(
			fasta => FASTA
		)

fromFastaToGenericSequence

Converts a sequence in Fasta format into a GenericSequence object.

 (sequence => GenericSequence) = fromFastaToGenericSequence 
		(
			fasta => FASTA
		)

fromFastaToNucleotideSequence

Converts a sequence in Fasta format into a NucleotideSequence object.

 (nucleotide => NucleotideSequence) = fromFastaToNucleotideSequence 
		(
			fasta => FASTA
		)

fromGenericToAminoAcidSequence

Converts a GenericSequence object into an AminoAcidSequence.

 (aminoacid => AminoAcidSequence) = fromGenericToAminoAcidSequence 
		(
			sequence => GenericSequence
		)

fromGenericToNucleotideSequence

Converts a GenericSequence object into a NucleotideSequence.

 (nucleotide => GenericSequence) = fromGenericToNucleotideSequence 
		(
			sequence => GenericSequence
		)

fromPDBTextToDSSP

Runs DSSP program to extract the secondary structure from the PDB input.

 (result => DSSP_Text) = fromPDBTextToDSSP 
		(
			pdbEntry => PDB__Text
		)

getAminoAcidSequence

Retrieves an aminoacid sequence from an aminoacid database.

 (sequence => AminoAcidSequence) = getAminoAcidSequence 
		(
			id => Object
		)

getCATHDomainNamesFromPDBID

Extracts CATH domain names from PDB ID.

 (CATH_domain_names => [Object]) = getCATHDomainNamesFromPDBID 
		(
			PDBID => Object
		)

getCDSSequence

Extract CDS sequences.

 (sequences => [NucleotideSequence]) = getCDSSequence 
		(
			input => Object
		)

getCodonTableFromEmboss

This is a utility to extract the Codon Usage Tables used by EMBOSS programs.

 (codon_usage_table => CodonUsageTable_Text) = getCodonTableFromEmboss 
		(
			table_name => Object
		)

getDocumentationFromProsite

Retrieves a documentation file from Prosite.

 (prosite_doc => PrositeDoc_Text) = getDocumentationFromProsite 
		(
			id => Object
		)

getDomainDescriptionFromCATH

Extracts domain definitions from CATH.

 (cath_doc => CathDomainDescription_XML) = getDomainDescriptionFromCATH 
		(
			CathDomainID => Object
		)

getEntryFromDSSP

Retrieves an entry from DSSP database.

 (entry => DSSP_Text) = getEntryFromDSSP 
		(
			id => Object
		)

getEntryFromEMBL

Retrieves an entry from EMBL database.

 (entry => EMBL_Text) = getEntryFromEMBL 
		(
			id => Object
		)

getEntryFromFSSP

Retrieves an entry from FSSP database.

 (entry => FSSP_Text) = getEntryFromFSSP 
		(
			id => Object
		)

getEntryFromGenBank

Retrieves an entry from GenBank database.

 (entry => GenBank_Text) = getEntryFromGenBank 
		(
			id => Object
		)

getEntryFromHSSP

Retrieves an entry from HSSP database.

 (entry => HSSP_Text) = getEntryFromHSSP 
		(
			id => Object
		)

getEntryFromPDB

Retrieves structures (whole PDB entries or single chains) from PDB database in PDB format.

 (entry => PDB__Text) = getEntryFromPDB 
		(
			id => Object
		)

getEntryFromPDBmmCIF

Provides a full PDB entry in mmCIF format.

 (entry => mmCIF_Text) = getEntryFromPDBmmCIF 
		(
			id => Object
		)

getEntryFromPfam

Retrieves an entry from Pfam database.

 (entry => HMM_Text) = getEntryFromPfam 
		(
			id => Object
		)

getEntryFromRefSeq

Retrieves an entry from RefSeq database.

 (entry => RefSeq_Text) = getEntryFromRefSeq 
		(
			id => Object
		)

getEntryFromSwissProt

Retrieves an entry from Swiss-Prot database.

 (entry => SwissProt_Text) = getEntryFromSwissProt 
		(
			id => Object
		)

getEntryFromTrEMBL

Retrieves an entry from TrEMBL database.

 (entry => SwissProt_Text) = getEntryFromTrEMBL 
		(
			id => Object
		)

getEntryFromUniProt

Retrieves an entry from UniProt database.

 (entry => SwissProt_Text) = getEntryFromUniProt 
		(
			id => Object
		)

getFastaSequence

Retrieves a sequence in Fasta format from a database.

 (sequence => FASTA) = getFastaSequence 
		(
			id => Object
		)

getNucleotideSequence

Retrieves a nucleotide sequence from a nucleotide database.

 (sequence => NucleotideSequence) = getNucleotideSequence 
		(
			id => Object
		)

parseBlastReportIntoHits

Extracts hits from a blast report.

 (hits => [Object]) = parseBlastReportIntoHits 
		(
			blast_report => BLAST__Text
		)

parsePDBIntoSeqs

Parses a PDB entry into its corresponding sequences.

 (sequence_chains => [GenericSequence]) = parsePDBIntoSeqs 
		(
			entry => Object
		)

parseSwissIntoPDBids

Extracts PDB ids from a Swiss-Prot entry.

 (ids => [Object]) = parseSwissIntoPDBids 
		(
			swiss_entry => SwissProt_Text
		)

runClustalwFast

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
		)

runClustalwFull

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
		)

runDGPIFromSequence

Analyzes protein sequences to find possible GPI-anchor sites.

 (dgpi_protein => DGPI_Report) = runDGPIFromSequence 
		(
			sequence => GenericSequence
		)

runDaliLite

Makes a pairwise structure comparison between two PDB chains.

 (dalilite_report => Structure_Alignment_Report) = runDaliLite 
		(
			entry1 => PDB__Text,
			entry2 => PDB__Text
		)

runDaliLiteAgainstPDB

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
		)

runEmbossAntigenicFromID

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
		)

runEmbossChargeFromID

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
		)

runEmbossCodcmpFromTables

Compares two codon usage tables.

 (codcmp_report => CodcmpReport_Text) = runEmbossCodcmpFromTables 
		(
			codon1 => CodonUsageTable_Text,
			codon2 => CodonUsageTable_Text
		)

runEmbossConsFromAlignment

Creates a consensus from multiple alignments.

 (consensus_sequence => Consensus_Sequence_Text) = runEmbossConsFromAlignment 
		(
			alignment => Sequence_alignment_report,
			identity => Integer,
			plurality => Integer,
			setcase => Integer,
			matrix => String
		)

runEmbossConsense

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
		)

runEmbossCpGplotFromID

Plots CpG rich areas.

 (CpGplot => Image_Encoded) = runEmbossCpGplotFromID 
		(
			usa => Object,
			to => Integer,
			window => Integer,
			from => Integer,
			minpc => Float,
			minoe => Float,
			minlen => Float
		)

runEmbossCpGreportFromID

Scans a nucletide sequence for higher than expected frequencies of the dinucleotide CG.

 (CpG => CpGReport) = runEmbossCpGreportFromID 
		(
			usa => Object,
			to => Integer,
			from => Integer,
			score => Integer
		)

runEmbossCuspFromID

Reads a CDS sequence and calculates a codon frequency table.

 (cusp_report => CodonUsageTable_Text) = runEmbossCuspFromID 
		(
			usa => Object,
			to => Integer,
			from => Integer
		)

runEmbossEmowse

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
		)

runEmbossEquicktandemFromID

Scans a sequence for potential tandem repeats.

 (repeats => EquicktandemReport) = runEmbossEquicktandemFromID 
		(
			usa => Object,
			to => Integer,
			threshold => Integer,
			from => Integer,
			maxrepeat => Integer
		)

runEmbossFindkm

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
		)

runEmbossGetorfFromID

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
		)

runEmbossNeedleFromIDs

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
		)

runEmbossOctanolFromID

Displays protein hydropathy.

 (octanol_report => Image_Encoded) = runEmbossOctanolFromID 
		(
			usa => Object,
			width => Integer,
			differenceplot => String,
			to => Integer,
			octanolplot => String,
			from => Integer,
			interfaceplot => String
		)

runEmbossPatmatdbFromID

Takes a protein motif and compares it to a protein sequence.

 (patmatdb_report => PatmatdbReport) = runEmbossPatmatdbFromID 
		(
			usa => Object,
			pattern => Pattern,
			to => Integer,
			from => Integer
		)

runEmbossPatmatmotifsFromID

Takes a protein sequence and compares it to the PROSITE database.

 (patmatmotifs_report => PatmatmotifsReport) = runEmbossPatmatmotifsFromID 
		(
			usa => Object,
			prune => String,
			to => Integer,
			from => Integer
		)

runEmbossPepcoilFromID

Coiled coil region prediction.

 (coil_prediction => Pepcoil_Text) = runEmbossPepcoilFromID 
		(
			usa => Object,
			to => Integer,
			from => Integer
		)

runEmbossPepinfoFromID

Detects and displays various metrics about a protein sequence.

 (pepinfo_report => PepinfoReport) = runEmbossPepinfoFromID 
		(
			usa => Object,
			hwindow => Integer,
			to => Integer,
			from => Integer
		)

runEmbossPepstatsFromID

Outputs a report of simple protein sequence information.

 (protein_statistics => Pepstats_Text) = runEmbossPepstatsFromID 
		(
			usa => Object,
			to => Integer,
			from => Integer
		)

runEmbossPepwindowFromID

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
		)

runEmbossPepwindowallFromSequences

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
		)

runEmbossRestrictFromID

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
		)

runEmbossSigcleaveFromID

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
		)

runEmbossTFscanFromID

Scans DNA sequences for transcription factors.

 (TF_prediction => TFscan_Text) = runEmbossTFscanFromID 
		(
			usa => Object,
			to => Integer,
			mismatch => Integer,
			from => Integer,
			menu => String
		)

runEmbossTmapSequenceFromID

Displays membrane spanning regions.

 (transmembrane_prediction => TransmembraneReport) = runEmbossTmapSequenceFromID 
		(
			usa => Object,
			to => Integer,
			from => Integer
		)

runEmbossTranseqFromID

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
		)

runEmbossWaterFromIDs

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
		)

runExtractCATHdomainsFromID

Creates the PDB files from the CATH domains especifications.

 (PDB_domains => [PDB__Text]) = runExtractCATHdomainsFromID 
		(
			domainID => [Object]
		)

runFastaForAminoAcids

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
		)

runFastaForNucleotides

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
		)

runFastf

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
		)

runFasts

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
		)

runHMMBuild

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
		)

runHMMPfam

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
		)

runHMMSearchAgainstDB

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
		)

runHMMSearchAgainstSeqs

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
		)

runLutefiskFromDTA

Infers the novo peptides from mass spectra using Lutefisk.

 (denovo_peptides => LutefiskReport) = runLutefiskFromDTA 
		(
			dta => DTA_Text
		)

runNCBIBlastn

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
		)

runNCBIBlastnXML

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
		)

runNCBIBlastn_2Seqs

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
		)

runNCBIBlastp

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
		)

runNCBIBlastpXML

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
		)

runNCBIBlastp_2Seqs

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
		)

runNCBIBlastx

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
		)

runNCBIBlastxXML

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
		)

runNCBIBlastx_2Seqs

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
		)

runNCBITBlastn

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
		)

runNCBITBlastnXML

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
		)

runNCBITBlastn_2Seqs

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
		)

runNCBITBlastx

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
		)

runNCBITBlastxXML

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
		)

runNCBITBlastx_2Seqs

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
		)

runPPSearchAgainstProsite

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
		)

runPSIBlast

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
		)

runPSIBlastXML

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
		)

runPepNovoFromDTA

Infers the novo peptides from mass spectra using PepNovo.

 (denovo_peptides => [PepNovoReport]) = runPepNovoFromDTA 
		(
			dta => [DTA_Text]
		)

runPhylipDnadist

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
		)

runPhylipDnaml

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
		)

runPhylipDnamlk

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
		)

runPhylipDnapars

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
		)

runPhylipDnapenny

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
		)

runPhylipFitch

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
		)

runPhylipKitsch

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
		)

runPhylipNeighbor

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
		)

runPhylipProtdist

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
		)

runPhylipProtpars

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
		)

runPratt

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
		)

runPs_scanAgainstProsite

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
		)

runPs_scanAgainstSequence

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
		)

runTcoffeeEvaluateAlignments

Evaluation of an alignment using Tcoffee.

 (tcoffee_evaluation => Clustalw_Evaluated_Text) = runTcoffeeEvaluateAlignments 
		(
			alignment => Clustalw_Text
		)

runTcoffeeFromProfiles

Makes a profile alignment using Tcoffee.

 (tcoffee_report => Clustalw_Text) = runTcoffeeFromProfiles 
		(
			alignments => [Clustalw_Text],
			profile_mode => String,
			clustalw_header => String,
			profile_comparison => String
		)

runTcoffeeFromSequences

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
		)

runWUBlastn

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
		)

runWUBlastn_2Seqs

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
		)

runWUBlastp

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
		)

runWUBlastp_2Seqs

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
		)

runWUBlastx

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
		)

runWUBlastx_2Seqs

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
		)

runWUTBlastn

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
		)

runWUTBlastn_2Seqs

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
		)

runWUTBlastx

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
		)

runWUTBlastx_2Seqs

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
		)

searchInterPro

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
		)

searchKeywordInUniProt

Searches entries from UniProt containing a specified keyword in one of the chosen fields.

 (description => [SequenceDescription_Text]) = searchKeywordInUniProt 
		(
			content => String,
			field => String
		)