NAME

pdg_cnb_uam_es.pm - Library for pdg_cnb_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 pdg_cnb_uam_es.

METHODS

fromFunCUTtoDASGFF

Transforms the output from the annotation service, FunCUT, into a file in xml format of distributed annotation system (DAS)

 (gffResult => DASGFF) = fromFunCUTtoDASGFF 
		(
			funcutResult => FunCUT_Annotation_XML
		)

fromNCutTextToNCutMatrix

Transforms the distance matrix of NCut from text format to xml format

 (ncutMatrix => NCut_Matrix) = fromNCutTextToNCutMatrix 
		(
			ncutInput => NCut_Text
		)

getDomainArchitectureByHMMPfam

Looks for known domains in a query sequence by searching the sequence against a HMM library (Pfam library)

 (prot_arch => DomainAnnotatedSequence) = getDomainArchitectureByHMMPfam 
		(
			prot_seq => AminoAcidSequence,
			tvalue => Float,
			evalue => Float,
			mode => String,
			cutoff_strategy => String
		)

getDomainArchitectureFromPfam

Gets the domain architecture of the proteins in Uniprot.

 (protein_arch => DomainAnnotatedSequence) = getDomainArchitectureFromPfam 
		(
			protein_ID => Object
		)

getInteractingMethods

It returns a list with the different methods where a protein ID is interacting

 (output => [Object]) = getInteractingMethods 
		(
			input => Object
		)

getInteractionMethodDesc

It returns the interaction method's description

 (output => InteractionMethod) = getInteractionMethodDesc 
		(
			input => Object
		)

getInteractions

It returns a list with the different interactions where a protein ID is interacting

 (output => [Interaction]) = getInteractions 
		(
			input => Object
		)

getInteractionsXML

It returns a list with the different IntAct_XML interactions where a protein IDs is interacting

 (output => [IntAct_XML]) = getInteractionsXML 
		(
			input => Object
		)

parseFromIntAct

Translates from IntAct XML format to BioMoby Interaction format

 (output => [Interaction]) = parseFromIntAct 
		(
			input => IntAct_XML
		)

parserISSReportIntoISSAnnotation

Parsers the complex report, 'ISS_Report', into the 'ISS_Annotation_XML' datatype

 (issXml => ISS_Annotation_XML) = parserISSReportIntoISSAnnotation 
		(
			issResult => ISS_Report
		)

parserISSReportIntoNCBIBlastText

Parsers the complex report, 'ISS_Report', into the 'NCBI_BLAST_Text' datatype

 (firstBlast => NCBI_BLAST_Text) = parserISSReportIntoNCBIBlastText 
		(
			issResult => ISS_Report
		)

parserISSReportIntoNCutMatrix

Parsers the complex report, ISS_Report, into the 'NCut_Matrix' datatype

 (ncutMatrix => NCut_Matrix) = parserISSReportIntoNCutMatrix 
		(
			issResult => ISS_Report
		)

runFASShtmlFromFASTA

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runFASShtmlFromFASTA 
		(
			FASTA_ArticleName_FASS => FASTA_AA_multi,
			gaps => Integer,
			cutoff => Float
		)

runFASShtmlFromMSF

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runFASShtmlFromMSF 
		(
			MSF_ArticleName_FASS => MSF,
			gaps => Integer,
			cutoff => Float
		)

runFASShtmlFromPIR

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runFASShtmlFromPIR 
		(
			PIR_ArticleName_FASS => PIR_Text,
			gaps => Integer,
			cutoff => Float
		)

runFASSxmlFromFASTA

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runFASSxmlFromFASTA 
		(
			FASTA_ArticleName_FASS => FASTA_AA_multi,
			gaps => Integer,
			cutoff => Float
		)

runFASSxmlFromMSF

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runFASSxmlFromMSF 
		(
			MSF_ArticleName_FASS => MSF,
			gaps => Integer,
			cutoff => Float
		)

runFASSxmlFromPIR

Automatic method for predicting functionally important residues in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runFASSxmlFromPIR 
		(
			PIR_ArticleName_FASS => PIR_Text,
			gaps => Integer,
			cutoff => Float
		)

runFunCUT

Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups)

 (funcutResult => FunCUT_Annotation_XML) = runFunCUT 
		(
			sequence => AminoAcidSequence,
			rounds => Integer,
			cutlen => Integer,
			evalue => Float,
			database => String,
			maxsearches => Integer,
			filters => String
		)

runISS

A sequence similitary search (NCBI Blast) is carried out to find proteins related to the query sequence

 (issResult => ISS_Annotation_XML) = runISS 
		(
			sequence => AminoAcidSequence,
			maxsearches => Integer,
			filters => String,
			rounds => Integer,
			cutlen => Integer,
			evalue => Float,
			database => String
		)

runISSComplete

A sequence similitary search (NCBI Blast) is carried out to find proteins related to the query sequence. Returns the matrix of distances, the first Blast report, and annotations of the proteins

 (issResult => ISS_Report) = runISSComplete 
		(
			sequence => AminoAcidSequence,
			rounds => Integer,
			cutlen => Integer,
			evalue => Float,
			filters => String,
			database => String,
			maxsearches => Integer
		)

runMBhtmlFromFASTA

Automatic method for predicting functionally important residues (Mutational Behavior) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runMBhtmlFromFASTA 
		(
			FASTA_ArticleName_MB => FASTA_AA_multi,
			residues => Integer,
			cutoff => Float
		)

runMBhtmlFromMSF

Automatic method for predicting functionally important residues (Mutational Behaviour) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runMBhtmlFromMSF 
		(
			MSF_ArticleName_MB => MSF,
			residues => Integer,
			cutoff => Float
		)

runMBhtmlFromPIR

Automatic method for predicting functionally important residues (mutational behavior) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runMBhtmlFromPIR 
		(
			PIR_ArticleName_MB => PIR_Text,
			residues => Integer,
			cutoff => Float
		)

runMBxmlFromFASTA

Automatic method for predicting functionally important residues (Mutational Behavior) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runMBxmlFromFASTA 
		(
			FASTA_ArticleName_MB => FASTA_AA_multi,
			cutoff => Float,
			residues => Integer
		)

runMBxmlFromMSF

Automatic method for predicting functionally important residues (Mutational Behaviour) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runMBxmlFromMSF 
		(
			MSF_ArticleName_MB => MSF,
			residues => Integer,
			cutoff => Float
		)

runMBxmlFromPIR

Automatic method for predicting functionally important residues (Mutational Behavior) in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runMBxmlFromPIR 
		(
			PIR_ArticleName_MB => PIR_Text,
			residues => Integer,
			cutoff => Float
		)

runNCut

Clustering application that groups the homolog sequences -subfamilies- and weights its closeness to the query sequence

 (ncutClusters => NCut_Clusters) = runNCut 
		(
			ncutMatrix => NCut_Matrix
		)

runOFunCUT

Analyzes the key functional annotations of the neighbor sequences related to the query sequence and makes the transference of the annotations, from clustering result (NCut) and sequence similitary search (ISSComplete, NCBI Blast)

 (funcutResult => FunCUT_Annotation_XML) = runOFunCUT 
		(
			firstBlast => NCBI_BLAST_Text,
			ncutClusters => NCut_Clusters,
			sequence => AminoAcidSequence,
			database => String
		)

runSMhtmlFromFASTA

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runSMhtmlFromFASTA 
		(
			FASTA_ArticleName_S => FASTA_AA_multi,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSMhtmlFromMSF

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runSMhtmlFromMSF 
		(
			MSF_ArticleName_S => MSF,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSMhtmlFromPIR

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_HTML => TreeDet_Annotation_HTML) = runSMhtmlFromPIR 
		(
			PIR_ArticleName_S => PIR_Text,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSMxmlFromFASTA

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the FASTA text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runSMxmlFromFASTA 
		(
			FASTA_ArticleName_S => FASTA_AA_multi,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSMxmlFromMSF

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the MSF text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runSMxmlFromMSF 
		(
			MSF_ArticleName_S => MSF,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSMxmlFromPIR

Automatic method for predicting functionally important residues using the concept of Relative Entropy in protein sequence alignments (longer than 50 residues and at least 15 sequences), in the PIR text format, as input.

 (treedetAnnotation_XML => TreeDet_Annotation_XML) = runSMxmlFromPIR 
		(
			PIR_ArticleName_S => PIR_Text,
			minsubfamily => Integer,
			secfamily => Integer,
			maxsubfamily => Integer
		)

runSquareFromFASTA

Produces a measure of per residue reliability for alignments between query sequences and sequences of known structure (ie those from the PDB), in the FASTA text format, as input.

 (squareAnnotation => TreeDet_Annotation_XML) = runSquareFromFASTA 
		(
			FASTA_ArticleName_SQ => FASTA_AA_multi,
			peakcutoff => Float,
			tail => Float,
			peakresidues => Integer
		)

runSquareFromMSF

Produces a measure of per residue reliability for alignments between query sequences and sequences of known structure (ie those from the PDB), in the MSF text format, as input.

 (squareAnnotation => TreeDet_Annotation_XML) = runSquareFromMSF 
		(
			MSF_ArticleName_SQ => MSF,
			peakresidues => Integer,
			tail => Float,
			peakcutoff => Float
		)

runSquareFromPIR

Produces a measure of per residue reliability for alignments between query sequences and sequences of known structure (ie those from the PDB), in the PIR text format, as input.

 (squareAnnotation => TreeDet_Annotation_XML) = runSquareFromPIR 
		(
			PIR_ArticleName_SQ => PIR_Text,
			peakresidues => Integer,
			tail => Float,
			peakcutoff => Float
		)