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Sequence_or_ID_or_GI

Workflow Entry: Sequence_or_ID_or_GI

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

Version 1 (of 1)

Version created on: 07/06/08 @ 16:58:14 by: Hamish McWilliam | Revision comments Expand

Title: Sequence_or_ID_or_GI

Type: Taverna 1

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Description

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.

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Option 2:

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Workflow Components

Inputs (1)

Name	Description
Sequence_or_ID_or_GI	Input sequence, GI number or entry identifier.

Processors (5)

Name	Type	Description
Sequence_or_ID	workflow	Get fasta formated sequence for an entry identifer or a sequence entry.
Get_fasta_from_GI	workflow	Get the sequence in fasta format for a GI number.
Is_GI	beanshell	Is the input a GI number?
Fail_if_GI	local	Fail if the sequence is a GI number.
Fail_if_sequence_or_id	local	Fail is the sequence is not a GI number.

Beanshells (3)

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
Build_fasta_seq		accver des seq	fasta_seq
Is_GI	Is the input a GI number?	gi_id_seq	is_gi

Outputs (1)

Name	Description
Sequence	Sequence in fasta format.

Links (7)

Source	Sink
Sequence_or_ID_or_GI	Get_fasta_from_GI:GI
Sequence_or_ID_or_GI	Is_GI:gi_id_seq
Sequence_or_ID_or_GI	Sequence_or_ID:Sequence_or_ID
Is_GI:is_gi	Fail_if_GI:test
Is_GI:is_gi	Fail_if_sequence_or_id:test
Get_fasta_from_GI:Sequence_fasta	Sequence
Sequence_or_ID:Sequence	Sequence

Coordinations (2)

Controller	Target
Fail_if_GI	Sequence_or_ID
Fail_if_sequence_or_id	Get_fasta_from_GI

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

Structure_or_ID

Information Tags (9)

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Information Shared with Groups (0)

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Information Featured In Packs (1)

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Information Ratings (0)

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Information Attributed By (1)

(Workflows/Files)

tRNAscan

Information Favourited By (0)

No one

Information Statistics

913 viewings

822 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Sequence_or_ID_or_GI

Created on: Saturday 07 June 2008 @ 16:58:14 (GMT)

Created by: Hamish McWilliam

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This Workflow only has one version.

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Tags (5):

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

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Attributions: Sequence_or_ID_or_GI

License: Creative Commons Attribution 3.0 Unported License

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Tags (6):