inb_bsc_es.pm - Library for inb_bsc_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 inb_bsc_es.
It converts a Clustalw data type into a Phylip Interleaved data type.
(phylip_alignment => Phylip_Interleaved_Text) = fromClustalwToPhylip ( clustalw_alignment => Clustalw_Text )
Retrieves an aminoacid sequence from an aminoacid database.
(sequence => AminoAcidSequence) = getAminoAcidSequence ( input => Object )
Retrieves an entry from a DSSP database.
(entry => DSSP_Text) = getEntryFromDSSP ( id => Object )
Retrieves an entry from an EMBL database.
(entry => EMBL_Text) = getEntryFromEMBL ( id => Object )
Retrieves an entry from a FSSP database.
(entry => FSSP_Text) = getEntryFromFSSP ( id => Object )
Retrieves an entry from GenBank database.
(entry => GenBank_Text) = getEntryFromGenBank ( id => Object )
Retrieves an entry from a HSSP database.
(entry => HSSP_Text) = getEntryFromHSSP ( id => Object )
Retrieves an entry from PDB database.
(entry => PDB__Text) = getEntryFromPDB ( id => Object )
Gets a HMM from Pfam given an ACC identifier.
(entry => HMM_Text) = getEntryFromPfam ( id => Object )
Retrieves an entry from RefSeq database.
(entry => RefSeq_Text) = getEntryFromRefSeq ( id => Object )
Retrieves an entry from SwissProt 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 )
Returns a sequence from uniprot annotated with all its features.
(sequence => FeatureAnnotatedAASequence) = getFeatureAASequenceFromUniprot ( id => Object )
Retrieves a nucleotide sequence from a nucleotide database.
(sequence => NucleotideSequence) = getNucleotideSequence ( input => Object )
ClustalW multiple sequence alignments (fast method).
(clustalw_report => Clustalw_Text) = runClustalwFast ( sequences => [GenericSequence], gapopen => Float, endgaps => String, gapdist => Integer, pairgap => Integer, matrix => String, topdiag => Integer, window => Integer, transitions_weight => Float, gapext => Float, ktup => Integer )
ClustalW multiple sequence alignments (full method).
(clustalw_report => Clustalw_Text) = runClustalwFull ( sequences => [GenericSequence], pwgapopen => Float, gapopen => Float, pwgapext => Float, gapdist => Integer, endgaps => String, matrix => String, gapext => Float, transitions_weight => Float, pwmatrix => String )
Makes a pairwise global alingment using the Needleman-Wunsch global alignment algorithm.
(pairwise_alignment => MSF) = runEmbossNeedleFromSequences ( sequence => GenericSequence, database => GenericSequence, gapextend => Float, datafile => String, gapopen => Float )
Pepinfo detects and displays various useful metrics about a protein sequence.
(pepinfo_report => PepinfoReport) = runEmbossPepinfoFromSequence ( sequence => AminoAcidSequence, hwindow => Integer, to => Integer, from => Integer )
Compares a protein sequence against a protein database using the FASTA algorithm.
(fasta_report => FASTA_Text) = runFastaForAminoAcids ( sequence => AminoAcidSequence, gap_open => Integer, alignments_number => Integer, high_scores_number => Integer, gap_extension => Integer, expectation_upper_value => Float, database => String, ktup => Integer, scoring_matrix => String )
Compares a nucleotide sequence (it is translated with frameshifts) against a protein database using the FASTA (fastx) algorithm.
(fasta_report => FASTA_Text) = runFastx ( sequence => NucleotideSequence, alignments_number => Integer, between_codon => Integer, high_scores_number => Integer, gap_extension => Integer, expectation_upper_value => Float, database => String, ktup => Integer, gap_open => Integer, scoring_matrix => String )
Compares a nucleotide sequence (it is translated with frameshifts and it allows frameshifts inside codons) against a protein database using the FASTA (fasty) algorithm.
(fasta_report => FASTA_Text) = runFasty ( sequence => NucleotideSequence, alignments_number => Integer, high_scores_number => Integer, database => String, gap_extension => Integer, expectation_upper_value => Float, ktup => Integer, within_codon => Integer, between_codon => Integer, gap_open => Integer, scoring_matrix => String )
It 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. Use this if you are trying to annotate an unknown sequence.
(hmmpfam_report => HMMPfam_Report) = runHMMPfam ( sequence => AminoAcidSequence, e__value_score => Integer, score_cutoff => Integer, alignment_number => Integer, e__value_domain => Float, hmm_accessions => String, score_cutoff_domain => Integer, e__value => Float )
Searches a set of sequences with a HMM profile.
(hmmsearch_report => HMMSearch_Report) = runHMMSearchAgainstSeqs ( profile => HMM_Text, sequences => [GenericSequence], e__value_score => Integer, score_cutoff => Integer, alignment_number => Integer, e__value_domain => Float, score_cutoff_domain => Integer, e__value => Float )
Compares a nucleotide sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastn ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, filter => String, extendgap => Integer, alignments => Integer, database => String, expect_threshold => Float, gapalign => String, opengap => Integer )
Compares a nucleotide sequence against another nucleotide sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
(bl2seq_report => BLAST__Text) = runNCBIBlastn_2Seqs ( database => NucleotideSequence, sequence => NucleotideSequence, gapalign => String, expect_threshold => Float, mismatch => Integer, match => Integer, word_size => Integer, extendgap => Integer, filter => String, dropoff => Integer, opengap => Integer )
Compares a protein sequence against a protein database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blast_report => BLAST__Text) = runNCBIBlastp ( sequence => AminoAcidSequence, opengap => Integer, gapalign => String, extendGap => Integer, expect_threshold => Float, database => String, alignments => Integer, matrix => String, filter => String, dropoff => Integer, scores => Integer )
Compares a protein sequence against another protein sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
(bl2seq_report => BLAST__Text) = runNCBIBlastp_2Seqs ( database => AminoAcidSequence, sequence => AminoAcidSequence, opengap => Integer, matrix => String, gapalign => String, word_size => Integer, extendgap => Integer, filter => String, expect_threshold => Float, dropoff => Integer )
Compares a nucleotide query sequence translated in all reading frames against a protein sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
(blastx_report => BLAST__Text) = runNCBIBlastx ( sequence => NucleotideSequence, opengap => Integer, gapalign => String, expect_threshold => Float, alignments => Integer, matrix => String, database => String, extendgap => Integer, filter => String, dropoff => Integer, scores => Integer )
Compares a nucleotide query sequence translated in all reading frames against a protein sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
(bl2seq_report => BLAST__Text) = runNCBIBlastx_2Seqs ( sequence => NucleotideSequence, database => AminoAcidSequence, dropoff => Integer, expect_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Compares an amino acid sequence against the six-frame translations of a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastn ( sequence => AminoAcidSequence, scores => Integer, dropoff => Integer, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, expect_threshold => Float, gapalign => String, opengap => Integer )
Compares a protein sequence against a nucleotide sequence (used as a database) dynamically translated in all six reading frames (both strands) using the Basic Local Alignment Tool (BLAST).
(bl2seq_report => BLAST__Text) = runNCBITBlastn_2Seqs ( sequence => AminoAcidSequence, database => NucleotideSequence, dropoff => Integer, expect_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).
(blast_report => BLAST__Text) = runNCBITBlastx ( sequence => NucleotideSequence, scores => Integer, dropoff => Integer, filter => String, extendgap => Integer, alignments => Integer, matrix => String, database => String, expect_threshold => Float, gapalign => String, opengap => Integer )
Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
(bl2seq_report => BLAST__Text) = runNCBITBlastx_2Seqs ( sequence => NucleotideSequence, database => NucleotideSequence, dropoff => Integer, expect_threshold => Float, filter => String, extendgap => Integer, word_size => Integer, gapalign => String, matrix => String, opengap => Integer )
Uses nucleotide sequences to compute a distance matrix, under four different models of nucleotide substitution.
(matrix => Distance_Matrix) = runPhylipDnadist ( alignment => Phylip_Text, basefrequency => String, matrix => String, freqt => Float, freqc => Float, freqg => Float, freqa => Float, method => String, ttratio => Float )
Estimates phylogenies from nucleotide sequences by unrooted parsimony.
(phylogenetic_tree => Newick_Text) = runPhylipDnapars ( alignment => Phylip_Text, randseed => Integer, random => String, threshold => Float, randtimes => Integer, 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, changeprob => Float, method => String, category => String, ttratio => Float, gencode => String )
Estimates phylogenies from protein sequences by unrooted parsimony.
(phylogenetic_tree => Newick_Text) = runPhylipProtpars ( alignment => Phylip_Text, outgroup_root => String, randtimes => Integer, threshold => Float, random => String, randseed => Integer, outgnum => Integer )
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 )
Multiple sequence alignment usinf T-coffee.
(tcoffee_report => Clustalw_Text) = runTcoffeeFromSequences ( sequences => [GenericSequence], gapopen => Integer, method => String, ndiag => Integer, tree_mode => String, ktuple => Integer, dp_mode => String, do_normalise => Integer, extend_mode => String, diag_mode => Integer, clustalw_header => String, gapext => Integer, extend => Integer )
It compares a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.
(wublastn_report => BLAST__Text) = runWUBlastn_2Seqs ( database => NucleotideSequence, sequence => 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, database => String, nogaps => String, matrix => String, alignments => Integer, scores => Integer, gap_extension => Integer, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, gap_open => Integer )
It compares a protein sequence against another protein sequence (used as a database) using the Washington University BLAST algorithm.
(wublastp_report => BLAST__Text) = runWUBlastp_2Seqs ( sequence => AminoAcidSequence, database => AminoAcidSequence, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, gap_extension => Integer, scores => 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) = runWUBlastx ( sequence => NucleotideSequence, gap_open => Integer, nogaps => String, database => String, alignments => Integer, matrix => String, statistics => String, word_size => Integer, filter => String, expected_threshold => Float, gap_extension => Integer, scores => Integer )
It compares a nucleotide query sequence translated in all reading frames against a protein sequence (used as a database) using the Washington University BLAST algorithm.
(wublastx_report => BLAST__Text) = runWUBlastx_2Seqs ( sequence => NucleotideSequence, database => AminoAcidSequence, 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 a protein sequence against a nucleotide sequence (used as a database) dynamically translated in all six reading frames (both strands) using the Washington University BLAST algorithm.
(wutblastn_report => BLAST__Text) = runWUTBlastn_2Seqs ( sequence => AminoAcidSequence, database => 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 a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.
(wutblastx_report => BLAST__Text) = runWUTBlastx_2Seqs ( database => NucleotideSequence, sequence => NucleotideSequence, expected_threshold => Float, filter => String, statistics => String, word_size => Integer, alignments => Integer, matrix => String, nogaps => String, gap_extension => Integer, scores => Integer, gap_open => Integer )