Workflow Entry: Nucleotide_ORF_translation

Created at: 06/06/08 @ 20:13:05

Version 1 (of 1)

Version created on: 06/06/08 @ 20:13:04 by: Hamish McWilliam | Revision comments Expand

Title: Nucleotide_ORF_translation

Type: Taverna 1

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Description

From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length.

EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).

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Workflow Components

Inputs (3)

Name	Description
Sequence_or_ID	Input nucleotide sequence. Either the actual sequence (fasta format) or an entry identifier in database:identifer format (e.g. embl:x01153).
Translation_table	The ID of the codon translation table to be used (e.g. 1).
Minimum_ORF_length	Minimum ORF length to report in base pairs (e.g. 240).

Processors (2)

Name	Type	Description
getorf	soaplabwsdl	Finds and extracts open reading frames (ORFs)
Sequence_or_ID	workflow	Ensure the sequence is in fasta format.

Outputs (1)

Name	Description
Translated_ORFs	Translations of the ORFs found.

Links (5)

Sink	Source
getorf:minsize	Minimum_ORF_length
Sequence_or_ID:Sequence_or_ID	Sequence_or_ID
getorf:sequence_direct_data	Sequence_or_ID:Sequence
getorf:table	Translation_table
Translated_ORFs	getorf:outseq