About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
Get homologous from an NCBI homoloGene.data file using a list of UniProt accessions

Workflow Entry: Get homologous from an NCBI homoloGene.data file using a list of UniProt accessions

Created at: 20/10/11 @ 17:53:28 Last updated: 27/10/11 @ 10:38:33

Version 1 (of 1)

Version created on: 20/10/11 @ 17:53:28 by: Rafael C. Jimenez | Revision comments Expand

Last edited on: 27/10/11 @ 10:38:39 by: Rafael C. Jimenez

Title: Get homologous from an NCBI homoloGene.data file using a list of UniProt accessions

Type: Taverna 2

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. This workflow is useful if you have a long list of protein accessions. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Download

Download Workflow File/Package (T2FLOW)

Download Workflow as a Galaxy tool

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/2498/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (3)

Name	Description
taxonomyAcc	Taxonomy accessions
uniprotAccessions	UniProt Protein accessions. Comma-separated values (CSV)
homologeneNcbiFile	Download homologene.data file from NCBI. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/

Processors (3)

Name	Type	Description
Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accession	workflow
Split_string_into_string_list_by_regular_expression	localworker
regex_value	stringconstant

Beanshells (8)

Name	Inputs	Outputs
getHomologousFrom_homoloGene	homologeneNcbiFile queryAccs specie	listOfResults
build_mapping_table	originalAccs crossReferenceAccs databaseNames taxonIds accessionVersions	results
newLine		newline
filterOutBlankResults	list1	list2
Beanshell	list1	list2
Beanshell_2	list1	list2
newLine_2		newline
Beanshell_2_2	list1	list2

Outputs (2)

Name	Description
homologous
ListOfUniprotAccessions

Datalinks (7)

Source	Sink
taxonomyAcc	Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accession:taxonomyAcc
Split_string_into_string_list_by_regular_expression:split	Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accession:proteinAccession
homologeneNcbiFile	Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accession:homologeneNcbiFile
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
uniprotAccessions	Split_string_into_string_list_by_regular_expression:string
Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accession:homologous	homologous
Split_string_into_string_list_by_regular_expression:split	ListOfUniprotAccessions

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Rafael C. Jimenez

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Rafael C. Jimenez

Information Attributions (0)

(Workflows/Files)

None

Information Tags (3)

Original 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 Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

54 viewings

84 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Get homologous from an NCBI homoloGene.data file using a list of UniProt accessions

Created on: Thursday 20 October 2011 @ 17:53:28 (GMT)

Created by: Rafael C. Jimenez

Last edited on: Thursday 27 October 2011 @ 10:38:39 (GMT)

Last edited by: Rafael C. Jimenez

Revision comments:

None

This Workflow only has one version.

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 (8)

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

Taverna 2

Original Uploader

Rafael C. Jimenez

Get homologous from NCBI homoloGene using a list of UniProt accessions (v1)

Created: 14/10/11 @ 17:45:28 | Last updated: 27/10/11 @ 10:39:21

Credits: Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 4 times

Tags (3):

View

Download (v1)

Taverna 2

Original Uploader

Rafael C. Jimenez

Get homologous from NCBI homoloGene using one UniProt accession (v1)

Created: 14/10/11 @ 17:26:32 | Last updated: 14/10/11 @ 17:26:28

Credits: Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 4 times

Tags (3):