Find orthologs using a uniprot accession

Created: 2011-10-14 13:07:41 Last updated: 2011-10-14 13:07:44

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Find orthologs based on ensembl information using as input/output uniprot accession

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Authors (1)

Titles (1)

Descriptions (1)

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Inputs (2)

Name	Description
uniprot_accessions	Just one uniprot Accession
orthologSpecie	Chose in which specie you want to find the orthologs. i.e human, mouse, rabbit, yeast

Processors (21)

Name	Type	Description
uniprot	biomart
Biomart_datasets_for_the_Ensembl_Genes_mart_service	workflow
Find_Orthologs_for_proteins_in_Ensembl	workflow
EBI_PICR__find_cross_references_for_protein_accessions	workflow
onlyActive_value	stringconstant	Value false
searchDatabases_value	stringconstant	Value SWISSPROT,TREMBL
Split_string_into_string_list_by_regular_expression	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
regex_value	stringconstant	Value ,
selectSecondColumn	localworker	Script if (!string.equals("")) { String regexString = "\t"; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); if(result.length > 2){ if(result[2].length() > 0){ mappedProtein = result[1] + "." + result[2]; } else { mappedProtein = result[1]; } } //for (int i = 0; i < result.length; i++) { // if(i==1){ // mappedProtein = result[i]; // } //} }
getTxId	wsdl	Wsdl http://xml.nig.ac.jp/wsdl/TxSearch.wsdl Wsdl Operation getTxId
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
seperator_value	stringconstant	Value
Merge_String_List_to_a_String_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
seperator_value_1	stringconstant	Value
Remove_String_Duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
Remove_String_Duplicates_2	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
Beanshell	beanshell	Script String newline = System.getProperty("line.separator");
Split_string_into_string_list_by_regular_expression_2	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
Merge_String_List_to_a_String_3	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
seperator_value_2	stringconstant	Value ,
String_List_Union	localworker	Script Set results = new HashSet(); for(Object list:lists){ results.addAll(list); } List union = new ArrayList(); union.addAll(results);

Beanshells (4)

Name	Inputs	Outputs
Beanshell		newline
GetDatasetsFromBiomartEnsemblGenes	species	datasetName datasetSpecie datasetDate datasetAssembly
findOrthologs	proteinId ensemblDataset idReference orthologSpecie	esemblId orthologId summary orthologyType homologSubtype homologPercId homologDs homologDn homologPercIdR1
build_mapping_table	originalAccs crossReferenceAccs databaseNames taxonIds accessionVersions	results

Outputs (1)

Name	Description
mappedProteins

Datalinks (26)

Source	Sink
uniprot_accessions	uniprot:uniprot.accession_filter
uniprot:uniprot.organism	Biomart_datasets_for_the_Ensembl_Genes_mart_service:species
orthologSpecie	Find_Orthologs_for_proteins_in_Ensembl:orthologSpecie
uniprot_accessions	Find_Orthologs_for_proteins_in_Ensembl:proteinId
Merge_String_List_to_a_String:concatenated	Find_Orthologs_for_proteins_in_Ensembl:ensemblDataset
Merge_String_List_to_a_String_2:concatenated	Find_Orthologs_for_proteins_in_Ensembl:idReference
onlyActive_value:value	EBI_PICR__find_cross_references_for_protein_accessions:onlyActive
Split_string_into_string_list_by_regular_expression:split	EBI_PICR__find_cross_references_for_protein_accessions:searchDatabases
getTxId:Result	EBI_PICR__find_cross_references_for_protein_accessions:taxonId
Remove_String_Duplicates:strippedlist	EBI_PICR__find_cross_references_for_protein_accessions:Protein_accessions
searchDatabases_value:value	Split_string_into_string_list_by_regular_expression:string
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
Split_string_into_string_list_by_regular_expression_2:split	selectSecondColumn:string
orthologSpecie	getTxId:tx_Name
seperator_value:value	Merge_String_List_to_a_String:seperator
Biomart_datasets_for_the_Ensembl_Genes_mart_service:datasetName	Merge_String_List_to_a_String:stringlist
uniprot:uniprot.entry_type	Merge_String_List_to_a_String_2:stringlist
seperator_value_1:value	Merge_String_List_to_a_String_2:seperator
Find_Orthologs_for_proteins_in_Ensembl:orthologId	Remove_String_Duplicates:stringlist
EBI_PICR__find_cross_references_for_protein_accessions:mapping_table	Remove_String_Duplicates_2:stringlist
Beanshell:newline	Split_string_into_string_list_by_regular_expression_2:regex
Remove_String_Duplicates_2:strippedlist	Split_string_into_string_list_by_regular_expression_2:string
seperator_value_2:value	Merge_String_List_to_a_String_3:seperator
String_List_Union:union	Merge_String_List_to_a_String_3:stringlist
selectSecondColumn:mappedProtein	String_List_Union:lists
Merge_String_List_to_a_String_3:concatenated	mappedProteins

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

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Rafael C. Jimenez

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Find orthologs using a uniprot accession

Created by Rafael C. Jimenez on Friday 14 October 2011 13:07:41 (UTC)

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Map a protein sequence to the known identifiers of identical sequences. Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping.

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Created: 2011-05-18 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Find orthologs using a uniprot accession

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