XNU and DNA-microsatellites

Keith Robison robison at mito.harvard.edu
Mon Sep 18 08:37:18 EST 1995

Jeffrey Keen (t.keen at ucl.ac.uk) wrote:
: Does anyone know whether it would be possible to use J-M Claveries XNU
: program to filter microsatellite regions out of DNA sequences, prior to
: database searches. 

: It presently is only suitable for masking low complexity segments out of
: protein sequences.

: Failing that - are there other programs I could use?

I believe XNU and SEG are unsuitable for this purpose.  

One solution to this is to build a database of microsatellite repeats,
and then pre-BLASTN your data against it (using relatively high
cutoffs to make sure you match only microsatellites), and then use
XBLAST to mask the matching regions (setting some parameter on
XBLAST so that it uses 'N' instead of 'X').  You'll probably have
to tune things a bit, but this has worked in the past for me.

Good luck!

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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