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
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