Hello -
There are not any specific utilities for dealing with this but
SoftMaskedAlphabet is just a standard biojava alphabet (with some
reworking of the internals) but can be used as normal. Hence, this should
work (I've not tested this so let me know if it doesn't).
//get a softmasked version of 'DNA'
FiniteAlphabet alpha = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
//Make a symbol list over that alphabet
SimpleSymbolList syms = new SimpleSymbolList(alpha.getTokenization(),
"ACCTCGCccccggggccccggggccccggggTTCGA");
//do stuff
...
- Mark
Douglas Hoen <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
08/29/2005 12:46 AM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] sequence masking?
Hi,
I want to mask out DNA subsequences, such as repetitive DNA. I have
been unable to find any APIs for this. I did find
SequenceTools.maskSequence(), but this method masks the region
outside an indicated location rather than inside it and it also uses
gaps as the mask symbol, whereas I would like to use N or lowercase.
Another related API is SoftMaskedAlphabet class, which seems useful
but I can't find any utilities that take advantage of it.
Any help would be appreciated. Thanks,
Doug
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
