Bioperl: Re: Bioperl-guts: repetitive DNA

[Ian Holmes]

Richard Durbin wrote code to do exactly this, I think. In the GCG package.
Is any part of that still free? Perhaps you could do a perl wrapper.

On Wed, 8 Sep 1999, Peter L. Schuerman wrote:

> Dear Listmembers,
> 
> I'm interested in finding a way to search for repetitive DNA arrays 
> in genomic sequence, and I was wondering if anyone had written a 
> module for this purpose.  It's fairly simple to search for repeats, 
> but I'm also interested in finding ones which are slightly imperfect 
> --- a few insertions, a few deletions, a few substitutions, e.g.:
> 
> ATATATATATATAT (normal)
> ATATATATTATAT (deletion of an A)
> ATATATATCATATAT (insertion of a C)
> ATATATGTATATAT (substitution of an A for a G)
> ATATTATATAATATAT (insertion and deletion)
> etc...
> 
> Is there a way to write a regular expression that is forgiving enough 
> to pick up arrays with these sorts of imperfections?
> 
> Regards,
> Peter L. Schuerman
> 
> Department of Biosciences
> 109 Tucker Hall
> University of Missouri at Columbia
> Columbia, MO 65211
> 
> office: schuermanp@missouri.edu           home: schuerman@biosci.org
>       "Who walks with truth, generates life." - Sumerian proverb
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