NAME

bioinfo_cipf_es.pm - Library for bioinfo_cipf_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 bioinfo_cipf_es.

METHODS

plotClustersProfilesAndTree

This service returns a PNG image representing a tree of clusters including their profiles

 (image => Image_Encoded) = plotClustersProfilesAndTree 
		(
			clusters => HierarchicalClustering
		)

plotClustersTree

This service returns a PNG image representing a tree of clusters

 (image => Image_Encoded) = plotClustersTree 
		(
			clusters => HierarchicalClustering
		)

runFatiGOplusCompare

runFatiGOplusSearch allows you to compare two lists of genes in terms of PubMed bio-entities (chimical and diseases), Gene Ontology terms (cellular component, biological process and molecular function), InterPro motifs, KEGG pathways, SwissProt keywords, Transcriptor factors, cis-regulatory elements (cisRED) and tissues.

 (histogram => Image_Encoded) = runFatiGOplusCompare 
		(
			list_1 => List_Text,
			list_2 => List_Text,
			database => String,
			terms => String
		)

runFatiGOplusGenomics

runFatiGOplusGenomics allows you to compare genes of a given chromosome region with the rest of the genome in terms of PubMed bio-entities (chimical and diseases), Gene Ontology terms (cellular component, biological process and molecular function), InterPro motifs, KEGG pathways, SwissProt keywords, Transcriptor factors, cis-regulatory elements (cisRED) and tissues.

 (histogram => Image_Encoded) = runFatiGOplusGenomics 
		(
			region => Object,
			terms => String,
			region_end_point => Integer,
			chromosome => String,
			database => String,
			region_start_point => Integer
		)

runFatiGOplusSearch

runFatiGOplusSearch allows you to annotate a single list of genes with Gene Ontology terms (cellular component, biological process and molecular function), InterPro motifs, KEGG pathways, SwissProt keywords, Transcriptor factors and cis-regulatory elements (cisRED).

 (histogram => Image_Encoded) = runFatiGOplusSearch 
		(
			list => List_Text,
			database => String,
			terms => String
		)

runHierarchicalClustering

Hierarchical clustering application for gene expression patterns using different conditions, methods and distances

 (clusters => HierarchicalClustering) = runHierarchicalClustering 
		(
			microarraydata => MicroArrayData_Text,
			distance => String,
			method => String,
			condition => String
		)

runSOTAClustering

A hierarchical unsupervised growing neural network based on Self-Organising Tree Algorithm (SOTA) for clustering gene expression patterns using different conditions and distances

 (clusters => HierarchicalClustering) = runSOTAClustering 
		(
			microarraydata => MicroArrayData_Text,
			distance => String,
			condition => String
		)