Workflow Entry: Homology workflow

Created at: 12/05/10 @ 07:31:32 Last updated: 12/05/10 @ 07:33:11

Version 1 (of 1)

Version created on: 12/05/10 @ 07:31:34 by: wabi | Revision comments Expand

Last edited on: 12/05/10 @ 07:33:12 by: wabi

Title: Homology workflow

Type: Taverna 2

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Description

There are many kinds of DNA data derived from many species in DDBJ. It makes possible to carry out the comparative study of genes of multiple species. The workflow provides a list of species and their genes that are similar to a human gene in response to a name of the human gene.

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http://www.myexperiment.org/workflows/1256/download?version=1
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Workflow Components

Authors (0)

Titles (1)

Descriptions (0)

Inputs (1)

Name	Description
human_gene_name	Specify name of a human gene

Processors (17)

Name	Type	Description
Make_query_for_searching_against_DDBJ_by_human_gene_name	beanshell
Get_DDBJ_list_by_ARSA_searchByXMLPath	localworker
Split_string_DDBJ_list_by_enter	localworker
Split_string_enter	stringconstant
Get_representative_accession	beanshell
Make_query_for_retrieving_sequence	beanshell
Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry	localworker
Make_query_for_BLAST	beanshell
Execute_BLAST	beanshell
Split_string_BLAST_result_by_enter	localworker
Get_accession_and_similarity_score_form_BLAST_result	beanshell
Make_query_for_retrieving_species_name	beanshell
Print_Result	beanshell
Get_species_name_by_ARSA_searchByXMLPath	localworker
database	stringconstant
param	stringconstant
Get_hit_count	beanshell

Beanshells (9)

Name	Inputs	Outputs
Make_query_for_searching_against_DDBJ_by_human_gene_name	geneName	url
Get_representative_accession	arsaResultLines	repAccession
Make_query_for_retrieving_sequence	accession	url
Make_query_for_BLAST	database dnaSeq param	query
Execute_BLAST	query baseUrl	contents
Get_accession_and_similarity_score_form_BLAST_result	lines	result
Make_query_for_retrieving_species_name	blastResult	url
Print_Result	organismNameResult accessionAndSimilarity arsaResultNum representiveAccession	result
Get_hit_count	arsaResultLines	hitCount

Outputs (1)

Name	Description
Species_name_that_has_orthologue_gene_and_accession_number_and_degree_of_similarity

Datalinks (22)

Source	Sink
human_gene_name	Make_query_for_searching_against_DDBJ_by_human_gene_name:geneName
Make_query_for_searching_against_DDBJ_by_human_gene_name:url	Get_DDBJ_list_by_ARSA_searchByXMLPath:url
Split_string_enter:value	Split_string_DDBJ_list_by_enter:regex
Get_DDBJ_list_by_ARSA_searchByXMLPath:contents	Split_string_DDBJ_list_by_enter:string
Split_string_DDBJ_list_by_enter:split	Get_representative_accession:arsaResultLines
Get_representative_accession:repAccession	Make_query_for_retrieving_sequence:accession
Make_query_for_retrieving_sequence:url	Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry:url
Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry:contents	Make_query_for_BLAST:dnaSeq
database:value	Make_query_for_BLAST:database
param:value	Make_query_for_BLAST:param
Make_query_for_BLAST:query	Execute_BLAST:query
Split_string_enter:value	Split_string_BLAST_result_by_enter:regex
Execute_BLAST:contents	Split_string_BLAST_result_by_enter:string
Split_string_BLAST_result_by_enter:split	Get_accession_and_similarity_score_form_BLAST_result:lines
Get_accession_and_similarity_score_form_BLAST_result:result	Make_query_for_retrieving_species_name:blastResult
Get_species_name_by_ARSA_searchByXMLPath:contents	Print_Result:organismNameResult
Get_hit_count:hitCount	Print_Result:arsaResultNum
Get_representative_accession:repAccession	Print_Result:representiveAccession
Get_accession_and_similarity_score_form_BLAST_result:result	Print_Result:accessionAndSimilarity
Make_query_for_retrieving_species_name:url	Get_species_name_by_ARSA_searchByXMLPath:url
Split_string_DDBJ_list_by_enter:split	Get_hit_count:arsaResultLines
Print_Result:result	Species_name_that_has_orthologue_gene_and_accession_number_and_degree_of_similarity