I saw some postings about this topic already on the list, but no "real" solution so far.
I take it that seqeunces are always handled in lowercase letters, so that basically biojava is unsuitable for working together with any algorythms that use soft masked sequences.
Is there any plan to actually change that in the near future, or is there already a solution that I missed?
Thanks for any comments Maik
P.S: When replying, please please please cc directly to me, too!
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