to find microsatellites...

Andy Law 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
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net