[Bioc-devel] Biostrings: ambiguous matching for 'compareStrings'

Julian Gehring julian.gehring at embl.de
Fri Mar 15 16:27:32 CET 2013


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

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