[Bioperl-l] Tandem Repeats Finder?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Sun Apr 13 22:53:46 EDT 2008


Scratch the need for a parser.
I turned off html output and it's all nice white-space separated text  :-)

Russell

> -----Original Message-----
> From: Smithies, Russell
> Sent: Monday, 14 April 2008 2:52 p.m.
> To: 'Bioperl BioPerl'
> Subject: Tandem Repeats Finder?
> 
> Has anyone tried TRF?
> I notice UCSC is using it for all their simple repeat annotations and thought it might
> be better than what we're currently using (Sputnik)
> 
> And is there a BioPerl parser for it's output or am I going to have to write my own ?
> 
> Thanx,
> 
> 
> Russell Smithies
> 
> Bioinformatics Applications Developer
> T +64 3 489 9085
>russell.smithies at agresearch.co.nz
> 
> Invermay  Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> T  +64 3 489 3809
> F  +64 3 489 9174
> www.agresearch.co.nz
> 

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