Hi Hannes, You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
But it will not stop when a maximal number of errors is reached ... JS Le 7 nov. 2011 à 15:42, Andreas Prlic a écrit : > Hi Hannes, > > you are right, this does not exist yet. Somebody else asked the same > question a few weeks ago. As such it would be great if you could > provide a patch, there might be other people interested in that, too. > > Andreas > > On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandstätter-Müller > <[email protected]> wrote: >> Following up: >> >> If there is no such thing, should I make it available if I write it? >> >> Hannes >> >> On Thu, Nov 3, 2011 at 14:08, Hannes Brandstätter-Müller >> <[email protected]> wrote: >>> Hi! >>> >>> Is there a Class/Method in Biojava that calculates the Levenshtein >>> distance between two sequences? I could not find anything in the docs >>> at first search. >>> >>> I need to compare 2 DNASequences (or Strings) and get the number of >>> insertions, deletions, and substitutions. Ideally, there would be an >>> option to abort the comparison if the number of mismatches exceeds a >>> certain number. >>> >>> Hannes >>> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
