Find orthologs using a uniprot accession

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

Download Workflow

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

Preview

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/2490/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

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

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Rafael C. Jimenez

Information Attributions (0)

(Workflows/Files)

None

Information Tags (3)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1867 viewings

1233 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Find orthologs using a uniprot accession

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

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (9)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

EBI_PICR_Sequence_to_ID (1)

Download

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.

Created: 2008-06-08

Credits: Hamish McWilliam

Taverna 2

Uploader

Rafael C. Jimenez

EBI PICR, find cross-references for protei... (2)

Download

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

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Value

Value

Script

Value

Script

Wsdl

Wsdl Operation

Script

Value

Script

Value

Script

Script

Script

Script

Script

Value

Script

Reviews (0)

Comments (0)

Other workflows that use similar services (9)