Find orthologs using a list of uniprot accessions

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

Download Workflow

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

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/2491/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
uniprotAccessions	A list of uniprot Accessions. Comma-separated values (CSV)
orthologEnsemblSpecieName	Specie name
orthologTaxId	Ortholog YTax ID for ENSEMBL 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
GetDatasetsFromBiomartEnsemblGenes	species	datasetName datasetSpecie datasetDate datasetAssembly
build_mapping_table	originalAccs crossReferenceAccs databaseNames taxonIds accessionVersions	results
findOrthologs	proteinId ensemblDataset idReference orthologSpecie	esemblId orthologId summary orthologyType homologSubtype homologPercId homologDs homologDn homologPercIdR1
Beanshell		newline

Outputs (2)

Name	Description
orthologous
listOfUniprotAccessions

Datalinks (7)

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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

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

2366 viewings

1436 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

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.

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 list of uniprot accessions

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Script

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (9)