>> 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.eduhttp://ibc.wustl.edu/~agarwal
Center for Computational Biology, Institute for Biomedical Computing
Washington University, Box 8036, 700 S. Euclid Avenue, St. Louis, MO 63110
