Bioperl-guts: repetitive DNA
Thu, 9 Sep 1999 17:51:05 +0100 (BST)
Peter Rice has rewritten Richard Durbin's "tandem"
for EMBOSS, with bug fixes. It's now called
I don't know how it's performance compares with
"dust" and "sputnik". The souce code should be
available under the GPL.
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: email@example.com home: firstname.lastname@example.org
> > "Who walks with truth, generates life." - Sumerian proverb
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