[Bioperl-l] How to use UTR

Barry Moore barry.moore at genetics.utah.edu
Tue Oct 14 11:30:19 EDT 2008


Grant,

To know where the UTRs are in your sequence you will need to have  
some kind of annotation associated with the sequence.  A couple of  
common sources for those annotations would be from a GenBank,  
ENSEMBL, or GFF3 - something that says there is a 3' UTR located  
between the locations 1,234 - 1,456 on your sequence.  Fasta sequence  
would normally not have that kind of information associated with it.   
You may need to rethink your source data.

You should have a look at a few of the very well written bioperl HOWTOs:

http://www.bioperl.org/wiki/HOWTO:Beginners
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Have a look through those documents to get an idea of how to handle  
sequences and annotations with bioperl, decide which approach applies  
best to your data, and then if you have more questions about how to  
implement the details drop us a line with more specifics about your  
situation.

Barry

Barry Moore
Senior Research Specialist
Eccles Institute of Human Genetics
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




On Oct 14, 2008, at 12:38 AM, liuganqiang wrote:

> Dear Hilmar Lapp,
>
>    I wanna to use bioperl to retrieve 3'UTR from a fasta sequence; but
> I don't know how to use  Bio::SeqFeature::Gene::UTR module. Could you
> show me some example script?
> Thank you very much!
> sincerely,
>
> Grant Liu
> 2008-10-14
>
> 各位明星之间什么关系?Live 人气榜为您悄然揭 
> 示。 现在就看看!<ATT00001.txt>




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