About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
Get homologous from NCBI homoloGene using one UniProt accession

Workflow Entry: Get homologous from NCBI homoloGene using one UniProt accession

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

Version 1 (of 1)

Version created on: 14/10/11 @ 17:26:32 by: Rafael C. Jimenez | Revision comments Expand

Title: Get homologous from NCBI homoloGene using one UniProt accession

Type: Taverna 2

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

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

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/2492/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (2)

Name	Description
proteinAccession	A UniProt protein Accession
taxonomyAcc	Specie where to find homologous. Use a taxonomy accession. Input "all" if you would like to find homologous in all the species.

Processors (22)

Name	Type	Description
EBI_PICR__find_cross_references_for_protein_accessions	workflow
onlyActive_value	stringconstant
taxonId_value	stringconstant
searchDatabases_value	stringconstant
Split_string_into_string_list_by_regular_expression_2	localworker
newLine	beanshell
getProteinRefSeqAcc	localworker
filterOutBlankResults	beanshell
Get_homologous_from_NCBI_homoloGene	workflow
Beanshell	beanshell
Beanshell_2	beanshell
EBI_PICR__find_cross_references_for_protein_accessions_2	workflow
Split_string_into_string_list_by_regular_expression	localworker
regex_value	stringconstant
string_value	stringconstant
onlyActive_value_1	stringconstant
Split_string_into_string_list_by_regular_expression_2_2	localworker
newLine_2	beanshell
selectSecondColumn	localworker
Beanshell_2_2	beanshell
Merge_String_List_to_a_String_3	localworker
seperator_value	stringconstant

Beanshells (8)

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

Outputs (1)

Name	Description
homologous

Datalinks (25)

Source	Sink
onlyActive_value:value	EBI_PICR__find_cross_references_for_protein_accessions:onlyActive
taxonId_value:value	EBI_PICR__find_cross_references_for_protein_accessions:taxonId
searchDatabases_value:value	EBI_PICR__find_cross_references_for_protein_accessions:searchDatabases
proteinAccession	EBI_PICR__find_cross_references_for_protein_accessions:Protein_accessions
EBI_PICR__find_cross_references_for_protein_accessions:mapping_table	Split_string_into_string_list_by_regular_expression_2:string
newLine:newline	Split_string_into_string_list_by_regular_expression_2:regex
Split_string_into_string_list_by_regular_expression_2:split	getProteinRefSeqAcc:string
getProteinRefSeqAcc:mappedProtein	filterOutBlankResults:list1
taxonomyAcc	Get_homologous_from_NCBI_homoloGene:specie
filterOutBlankResults:list2	Get_homologous_from_NCBI_homoloGene:proteinAccs
Get_homologous_from_NCBI_homoloGene:Beanshell_listOfResults	Beanshell:list1
Beanshell:list2	Beanshell_2:list1
Split_string_into_string_list_by_regular_expression:split	EBI_PICR__find_cross_references_for_protein_accessions_2:searchDatabases
onlyActive_value_1:value	EBI_PICR__find_cross_references_for_protein_accessions_2:onlyActive
Beanshell_2:list2	EBI_PICR__find_cross_references_for_protein_accessions_2:Protein_accessions
taxonomyAcc	EBI_PICR__find_cross_references_for_protein_accessions_2:taxonId
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
string_value:value	Split_string_into_string_list_by_regular_expression:string
EBI_PICR__find_cross_references_for_protein_accessions_2:mapping_table	Split_string_into_string_list_by_regular_expression_2_2:string
newLine_2:newline	Split_string_into_string_list_by_regular_expression_2_2:regex
Split_string_into_string_list_by_regular_expression_2_2:split	selectSecondColumn:string
selectSecondColumn:mappedProtein	Beanshell_2_2:list1
Beanshell_2_2:list2	Merge_String_List_to_a_String_3:stringlist
seperator_value:value	Merge_String_List_to_a_String_3:seperator
Merge_String_List_to_a_String_3:concatenated	homologous

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

67 viewings

106 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Get homologous from NCBI homoloGene using one UniProt accession

Created on: Friday 14 October 2011 @ 17:26:32 (GMT)

Created 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):