you could send it to the list here and ask for feedback.. Andreas
On Tue, Nov 15, 2011 at 6:10 AM, Hannes Brandstätter-Müller <[email protected]> wrote: > Well, I have implemented a first version that is running quite well > for me and my needs/specifications, although I did not integrate it > directly into the biojava class hierarchy yet. > Is anyone interested in taking a look at it and giving me some > feedback if I shoud invest the time and work to make it includable > into biojava? > > Hannes > > On Wed, Nov 9, 2011 at 10:01, Hannes Brandstätter-Müller > <[email protected]> wrote: >> 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 > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
