[Biococoa-dev] BCScanner

John Timmer jtimmer at bellatlantic.net
Wed Mar 16 14:24:55 EST 2005

>> BCSequence
>> Pocessed by BCFindSequence -> array of ranges
>> BCSequence  subSequenceInRange -> individual digest fragments
>> A scanner seems like overkill for this need.
> The nice thing of a scanner is that you can pass it a
> symbolset/characterset, containing all the various locations where a
> sequence has to be cut. At least this is how I use it for proteins in
> my own app. Eg trypsin cuts at K and R, if we pass KR to findSequence,
> it will look for that actual sequence. If we pass it as a symbolset to
> a scanner, it will look for each individual symbol, which is what we
> want.

Ah, I hadn't thought of that case.  I keep thinking in nucleotide terms,
where every possible combination of nucleotides is represented by a single
symbol.  This might be another case where splitting the tool two ways (one
for aa's, one for nt's) could be justified by performance profiling.


This mind intentionally left blank

More information about the Biococoa-dev mailing list