Bioperl-guts: repetitive DNA

[James Gilbert]

Hi,

Peter Rice has rewritten Richard Durbin's "tandem"
for EMBOSS, with bug fixes.  It's now called
"etandem":

http://www.sanger.ac.uk/Software/EMBOSS/Apps/etandem.shtml

I don't know how it's performance compares with
"dust" and "sputnik".  The souce code should be
available under the GPL.

	James

On Wed, 8 Sep 1999, Ian Holmes wrote:

> 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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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919


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