XNU and DNA-microsatellites
agarwal at ibc.ibc.wustl.edu
Mon Sep 18 13:04:35 EST 1995
>> In article <43jsme$8gd at decaxp.harvard.edu> robison at mito.harvard.edu (Keith Robison) writes:
>> 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.
Actually XNU (or rather its nucleotide counterpart XNUN) is extremely
suitable for filtering out ALL microsatellite regions. In fact, it
only filters out all tandem repeats with period < 9 (default). The
period is adjustable. For example, setting it to 1 will only filter
out all the poly-nucleotide tracts.
>> 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.
Keith's suggestion is superior, if you want to just filter out a few
Pankaj Agarwal Postdoctoral Research Associate
agarwal at ibc.wustl.edu http://ibc.wustl.edu/~agarwal
Center for Computational Biology, Institute for Biomedical Computing
Washington University, Box 8036, 700 S. Euclid Avenue, St. Louis, MO 63110
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