tRNAscan

Created: 2008-06-28 09:57:33

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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).

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Workflow Components

Inputs (2)

Name	Description
Sequence_or_ID_or_GI	Input nucleotide sequence to search for tRNA genes. This can be one of: - Actual sequence (fasta format recommended) - Entry identifier in database:identifer format (e.g. EMBL:AB005233) - NCBI GI number (e.g. 2264305)
Sequence_origin	The tRNAscan tool needs to know the type of tRNA signature to search for (e.g. Eukaryotic tRNAs). Possible values are: - Eukaryotic tRNAs - Bacterial tRNAs - Eukaryotic tRNAs - Archaeal tRNAs - Mitochondrial/Chloroplast tRNAs - General tRNAs

Processors (2)

Name	Type	Description
getTRNA	arbitrarywsdl	Run tRNAscan.
Sequence_or_ID_or_GI	workflow	Get a fasta formated sequence for one of: 1. Actual sequence in an EMBOSS supported format (see http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in). 2. Sequence entry identifer in database:identifer format. Retreived using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). 3. An NCBI GI number. Retrived using NCBI's eUtils web service (see http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html)

Beanshells (3)

Name	Description	Inputs	Outputs
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

Outputs (1)

Name	Description
tRNAscan_output	The tRNAscan result in the DAS XML format (see http://www.biodas.org/documents/spec.html).

Links (4)

Source	Sink
Sequence_or_ID_or_GI	Sequence_or_ID_or_GI:Sequence_or_ID_or_GI
Sequence_or_ID_or_GI:Sequence	getTRNA:in0
Sequence_origin	getTRNA:in1
getTRNA:getTRNAReturn	tRNAscan_output

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Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Information Credits (1)

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Hamish McWilliam

Information Attributions (1)

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Sequence_or_ID_or_GI

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Information Statistics

2645 viewings

2338 downloads

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tRNAscan

Created by Hamish McWilliam on Saturday 28 June 2008 09:57:33 (UTC)

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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.

Created: 2008-06-07 | Last updated: 2008-06-07

Credits: Hamish McWilliam

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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