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NCBI_QBLAST

Workflow Entry: NCBI_QBLAST

Created at: 07/06/08 @ 15:05:00 Last updated: 07/06/08 @ 17:11:36

Version 2 (latest) (of 2)

Version created on: 07/06/08 @ 15:05:00 by: Hamish McWilliam | Revision comments Expand

Last edited on: 07/06/08 @ 17:11:36 by: Hamish McWilliam

Title: NCBI_QBLAST

Type: Taverna 1

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Description

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

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Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (0)

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None

Information Tags (5)

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Information Statistics

693 viewings

1527 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - NCBI_QBLAST

Created on: Saturday 07 June 2008 @ 15:05:00 (GMT)

Created by: Hamish McWilliam

Revision comments:

None

Latest Version:
[2] - NCBI_QBLAST

Created on: Saturday 07 June 2008 @ 15:05:00 (GMT)

Created by: Hamish McWilliam

Last edited on: Saturday 07 June 2008 @ 17:11:36 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

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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Other workflows that use similar services (42)

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

Taverna 1

Original Uploader

Hamish McWilliam

Sequence_or_ID_or_GI (v1)

Created: 07/06/08 @ 16:58:14

Credits: Hamish McWilliam

Attributions: Structure_or_ID

License: Creative Commons Attribution 3.0 Unported License

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.

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

Viewed: 118 times | Downloaded: 60 times

Tags (9):

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Taverna 1

Original Uploader

Hamish McWilliam

tRNAscan (v1)

Created: 28/06/08 @ 09:57:33

Credits: Hamish McWilliam

Attributions: Sequence_or_ID_or_GI

License: Creative Commons Attribution 3.0 Unported License

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).

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

Viewed: 152 times | Downloaded: 56 times

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