to find microsatellites...
Andy.Law at bbsrc.ac.uk
Wed Nov 26 04:46:39 EST 1997
In article <65f2m5$5np$1 at oravannahka.Helsinki.FI>, Sampo H Smolander
<ssmoland at cc.helsinki.fi> wrote:
> Do you know about programs that would scan sequence data
> to find microsatellites (i.e. short tandem repeats) ?
> Such a program would be pretty simple (I guess I'd make
> one in a week), so I am a bit amazed because I couldn't
> find anything after a considerable time spent for searching...
You can use the xnun program (Claverie & States, 1993 Computers Chem. 17
191-201), with a couple of modifications. xnu/xnun are filters to mask out
regions of "low complexity". I have modified a version of it to report,
rather than mask, those regions. You can have a copy if you want it.
Note: You still have to look at the bits it has reported and decide
yourself if it is a microsatellite or not, but it is a start.
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )
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