Find orthologs using a list of uniprot accessions

Created: 2011-10-14 13:12:36 Last updated: 2014-06-03 17:39:32

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

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Authors (1)

Titles (1)

Descriptions (1)

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Inputs (2)

Name	Description
uniprotAccessions	A list of uniprot Accessions. Comma-separated values (CSV)
orthologSpecie	Specie name

Processors (3)

Name	Type	Description
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 ,
Find_orthologs_using_a_uniprot_accession	workflow

Beanshells (4)

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

Outputs (2)

Name	Description
orthologous
listOfUniprotAccessions

Datalinks (6)

Source	Sink
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
uniprotAccessions	Split_string_into_string_list_by_regular_expression:string
orthologSpecie	Find_orthologs_using_a_uniprot_accession:orthologSpecie
Split_string_into_string_list_by_regular_expression:split	Find_orthologs_using_a_uniprot_accession:uniprot_accessions
Find_orthologs_using_a_uniprot_accession:mappedProteins	orthologous
Split_string_into_string_list_by_regular_expression:split	listOfUniprotAccessions

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Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

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Rafael C. Jimenez

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2264 viewings

1352 downloads

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Version History

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Find orthologs using a list of uniprot accessions

Created by Rafael C. Jimenez on Friday 14 October 2011 13:12:36 (UTC)
Find orthologs using a list of uniprot accessions

Created by Rafael C. Jimenez on Tuesday 03 June 2014 17:39:32 (UTC)

Revision comment:

Workflow fixed. ENSEMBL Biomart changed attributes breaking the workflow and japanese webservice to get TaxIDs is not longer available.

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

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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 list of uniprot accessions

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Other workflows that use similar services (9)