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GetUtrSeq

Fetch UTR sequences of query transcripts. It can support both 5' and 3' UTRs.

Version 1.0
Bundle sequencing
Categories smallRNA
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires Ensembl Perl API
Source files component.xml GetUtrSeq.pl
Usage Example with default values

Inputs

Name Type Mandatory Description
transcripts CSV Mandatory Transcript Ensembl IDs.
connection Properties Mandatory Connection parameters of Ensembl database, including host, database, port, user and driver information.

Outputs

Name Type Description
UTR5 FASTA 5' UTR sequences in FASTA format.
UTR3 FASTA 3' UTR sequences in FASTA format.

Parameters

Name Type Default Description
primeType string "3prime" The type of UTR regions to be fetched. It could be one of '5prime', '3prime' or both.

Test cases

Test case Parameters IN
transcripts
IN
connection
OUT
UTR5
OUT
UTR3
case1 (missing) transcripts connection UTR5 UTR3

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