NCBI_QBLAST

Created: 2008-06-07 15:05:00 Last updated: 2008-06-07 17:11:36

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Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

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Workflow Components

Inputs (3)

Name	Description
Sequence_or_ID_or_GI	Input sequence. Either the actual sequence, an NCBI GI identifer (e.g. 75251068 or 1531757) or an entry identifier in database:identifer format (e.g. uniprot:AUX1_ARATH or embl:X98772).
Search_database	Database to search (e.g. nr or nt).
BLAST_program	NCBI BLAST "program" to use for the search (e.g. blastp or blastn).

Processors (4)

Name	Type	Description
QBLAST_Put	workflow	Submit the QBLAST job.
QBLAST_Get	workflow	Check if the QBLAST job has finished, and get results.
Sequence_or_ID_or_GI	workflow
Reformat_sequence	beanshell

Beanshells (9)

Name	Description	Inputs	Outputs
Build_QBLAST_Put_URL	Build QBLAST put URL.	program database query_sequence	put_url
Extract_QBLAST_job_ID	Extract the QBLAST job identifer from the response.	qblast_output	job_id
Extract_QBLAST_status	Extract the job status from the QBLAST output.	qblast_output	qblast_status
Build_QBLAST_Get_URL	Build the URL to get the job status/results	job_id	get_url
Is_done	Map the job status into true/false.	job_status	is_done
Build_fasta_seq		accver des seq	fasta_seq
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence
Is_GI	Is the input a GI number?	gi_id_seq	is_gi
Reformat_sequence		in_seq	out_seq

Outputs (2)

Name	Description
NCBI_QBLAST_job_ID	NCBI QBLAST job identifer.
NCBI_QBLAST_result	NCBI BLAST result from QBLAST. This is similar to the normal NCBI BLAST output but contains some HTML/XML tags.

Links (8)

Source	Sink
BLAST_program	QBLAST_Put:BLAST_program
Search_database	QBLAST_Put:BLAST_database
QBLAST_Put:QBLAST_job_ID	QBLAST_Get:QBLAST_job_ID
Sequence_or_ID_or_GI	Sequence_or_ID_or_GI:Sequence_or_ID_or_GI
Reformat_sequence:out_seq	QBLAST_Put:Query_sequence
Sequence_or_ID_or_GI:Sequence	Reformat_sequence:in_seq
QBLAST_Get:QBLAST_result	NCBI_QBLAST_result
QBLAST_Put:QBLAST_job_ID	NCBI_QBLAST_job_ID

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Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Hamish McWilliam

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Information Statistics

3287 viewings

3223 downloads

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Version History

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NCBI_QBLAST

Created by Hamish McWilliam on Saturday 07 June 2008 15:05:00 (UTC)
NCBI_QBLAST

Created by Hamish McWilliam on Saturday 07 June 2008 15:05:00 (UTC)

Last edited by Hamish McWilliam on Saturday 07 June 2008 17:11:36 (UTC)

Revision comment:

Add support for getting the query sequence from an NCBI GI number or an entry identifier in database:identifier format. Also reformat the sequence before attempting to put it in the QBLAST Put URL.

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Taverna 1

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Hamish McWilliam

Sequence_or_ID_or_GI (1)

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Get a sequence in fasta format given one of: An NCBI GI number (e.g. 75251068). An entry identifier in database:identifier format (e.g. uniprot:Q96247). 3. A sequence entry in a format supported by EMBOSS seqret.

Created: 2008-06-07

Credits: Hamish McWilliam

Attributions: Structure_or_ID

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tRNAscan (1)

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Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE). This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).

Created: 2008-06-28

Credits: Hamish McWilliam

Attributions: Sequence_or_ID_or_GI