XNU and DNA-microsatellites

Pankaj Agarwal 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
specific microsatellites.

Pankaj
--
--
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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