genome_imim_es.pm - Library for genome_imim_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 genome_imim_es.
Converts aminoacid FASTA sequence into an aminoacid sequence
(sequence => AminoAcidSequence) = fromFASTAToAminoAcidSequence ( sequence => FASTA_AA )
Converts aminoacid FASTA sequences into a collection of aminoacid sequences
(sequences => [AminoAcidSequence]) = fromFASTAToAminoAcidSequenceCollection ( sequences => FASTA_AA_multi )
Converts a DNA FASTA sequence into a DNA sequence
(sequence => DNASequence) = fromFASTAToDNASequence ( sequence => FASTA_NA )
Converts DNA FASTA sequences into a collection of DNA sequences
(sequences => [DNASequence]) = fromFASTAToDNASequenceCollection ( sequences => FASTA_NA_multi )
Converts a collection of generic sequences into FASTA sequences
(sequences => FASTA) = fromGenericSequenceCollectionToFASTA ( sequences => [GenericSequence] )
Converts a generic sequence into a FASTA sequence
(sequence => FASTA) = fromGenericSequenceToFASTA ( sequence => GenericSequence )
Parses a collection of meta-alignment outputs to produce a sequence similarity score matrix
(matrix => Distance_Matrix) = fromMetaAlignmentsToScoreMatrix ( similarity_results => [Meta_Alignment_Text] )
Parses a collection of meta-alignment outputs to produce a text-formatted sequence similarity score matrix
(microarraydata => MicroArrayData_Text) = fromMetaAlignmentsToTextScoreMatrix ( similarity_results => [Meta_Alignment_Text] )
Parses the score or probability motif matrices from MEME output
(motif_weight_matrices => [Matrix]) = parseMotifMatricesFromMEME ( meme_predictions => MEME_Text, matrixmode => String )
Ab initio gene prediction tool that returns the gene predictions in GFF format.
(geneid_predictions => GFF) = runGeneIDGFF ( sequence => DNASequence, engine => String, strand => String, exons => String, signals => String, profile => String )
Analyzes a DNA sequence for putative transcription factor binding sites from Transfac or Jaspar and reports them in GFF format
(matscan_predictions => GFF) = runMatScanGFF ( sequence => DNASequence, matrixmode => String, motifdatabase => String, strand => String, threshold => Float )
Analyzes a collection of DNA sequences for putative transcription factor binding sites from Transfac or Jaspar and reports them in GFF format
(matscan_predictions => [GFF]) = runMatScanGFFCollection ( sequences => [DNASequence], motifdatabase => String, strand => String, threshold => Float, matrixmode => String )
Analyzes a collection of DNA sequences for putative motifs (transcription or splicing factor binding sites) and reports them in GFF format. The collection of motifs is given by the user as a set of Position Weight Matrices (PWMs)
(matscan_predictions => [GFF]) = runMatScanGFFCollectionVsInputMatrices ( sequences => [DNASequence], motif_weight_matrices => [Matrix], strand => String, threshold => Float, matrixmode => String )
Analyzes a set of protein or DNA sequences for similarities among them and produces a description (motif) for each pattern it discovers. The results are returned in HTML format
(meme_predictions => text_html) = runMemeHTML ( sequences => [GenericSequence], minimumsitesforeachmotif => Integer, maximumnumberofmotifs => Integer, motifdistribution => String, backgroundmarkovmodeltrainingvalueisthemodelorder => String, motifE__valuecutoff => String, maximumsitesforeachmotif => Integer, maximumoptimumwidth => Integer, minimumoptimumwidth => Integer )
Analyzes a set of protein or DNA sequences for similarities among them and produces a description (motif) for each pattern it discovers. The results are returned in MEME text format
(meme_predictions => MEME_Text) = runMemeText ( sequences => [GenericSequence], minimumsitesforeachmotif => Integer, maximumnumberofmotifs => Integer, motifdistribution => String, backgroundmarkovmodeltrainingvalueisthemodelorder => String, motifE__valuecutoff => String, maximumsitesforeachmotif => Integer, maximumoptimumwidth => Integer, minimumoptimumwidth => Integer )
Produces alignments of sequences of TF binding sites and returns the predictions in 'Meta-alignment' format. You can use runMatScanGFF to produce the input GFF files, specifying the 'log-likelihood' matrix mode.
(meta_predictions => Meta_Alignment_Text) = runMetaAlignment ( map2 => GFF, map1 => GFF, lambapenalty => Float, mupenalty => Float, alphapenalty => Float )
Produces alignments of sequences of TF binding sites and returns the predictions in GFF format. You can use runMatScanGFF to produce the input GFF files, specifying the 'log-likelihood' matrix mode
(meta_predictions => GFF) = runMetaAlignmentGFF ( map2 => GFF, map1 => GFF, lambapenalty => Float, mupenalty => Float, alphapenalty => Float )
Runs Meta-alignment software on a multiple running mode, receiving a collection of maps, making pairs of them and, foreach pair, producing, in 'Meta-alignment' format, alignments of sequences of TF binding sites
(meta_predictions => [Meta_Alignment_Text]) = runMultiPairwiseMetaAlignment ( maps => [GFF], lambapenalty => Float, alphapenalty => Float, mupenalty => Float )
Runs Meta-alignment software on a multiple running mode, receiving a collection of maps, making pairs of them and, foreach pair, producing, in GFF format, alignments of sequences of TF binding sites
(meta_predictions => [GFF]) = runMultiPairwiseMetaAlignmentGFF ( maps => [GFF], lambapenalty => Float, mupenalty => Float, alphapenalty => Float )
Ab initio gene prediction service that runs geneid with synteny evidences and returns the output predictions in GFF format. To generate the synteny evidences, use a tblastx service
(geneid_predictions => GFF) = runSGP2GFF ( sequence => DNASequence, tblastx_report => BLAST__Text, profile => String )
Translates the GeneID gene predictions, given in GFF format, into a set of aminoacid sequences
(peptides => [AminoAcidSequence]) = translateGeneIDGFFPredictions ( geneid_predictions => GFF, sequence => DNASequence, translationtable => String )