Bioperl: repetitive DNA
Thu, 09 Sep 1999 09:26:39 +0100
Hi. I think a good solution could also be to use NCBI's DUST
filter with a suitable cut-off, then retrieve the coordinates
of masked sequences through a perl wrapper - c'est fait.
You can retrieve DUST from WU ftp server:
dust test 45
BTW, I think that this could be a good startup for a "filtering"
module. Do you think this could be interesting ? It could be a
method in a sequence object or a separate module per se. The outcome
could be a list of coordinates in the sequence which correspond to
masked areas. I would be happy to produce a rough version of this.
Alessandro Guffanti - Informatics
The Sanger Centre, Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SA, United Kingdom
phone: +1223-834244 * fax: +1223-494919
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