Hi,
When I want to compare two aligned sequences of the same length and find
the mismatching positions, 'compareStrings' from the 'Biostrings'
package seems to be the best choice. However, it does take into account
any ambiguous matches (as matching any base to 'N'), as it can be found
with the 'fixed' for 'matchPattern' and related functions. Would it be
reasonable to include this, to ensure a consistent behavior of methods
for 'XString' and related objects?
Best wishes
Julian
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