Nucleotide_ORF_translation

Created: 2008-06-06 20:13:04

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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.

Beanshells (1)

Name	Description	Inputs	Outputs
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

Outputs (1)

Name	Description
Translated_ORFs	Translations of the ORFs found.

Links (5)

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

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Hamish McWilliam

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Hamish McWilliam

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Sequence_or_ID

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Nucleotide_InterProScan

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Nucleotide_ORF_translation

Created by Hamish McWilliam on Friday 06 June 2008 20:13:04 (UTC)

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