Thanks. I am thinking about implementing a modified MatrixAligner to fit my needs here. Direct Levenstein Distance is not exactly right for my application, because there are 0 to n insertions/deletions.
A direct LevensteinDistance as implemented in would not give me all the Information I need. Thanks for the hints and input. Hannes PS we seriously need more examples in the Cookbook - I'll submit some later, but the modified N-W Aligner mentioned below would make a good example too, don't you think? ;) On Mon, Nov 7, 2011 at 16:03, <[email protected]> wrote: > 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
