Bioperl: repetitive DNA

Alessandro Guffanti
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

dust test 45

Best Wishes,


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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