Did you try to align the sequences first? That would also give you the number of identical nucleotides.
Andreas On Thu, Dec 22, 2011 at 1:18 AM, Hannes Brandstätter-Müller <[email protected]> wrote: > Hi! > > I recently ran into the problem of having 2 very similar DNA Sequences > and wanting to get (1) a difference count and (2) a consensus > sequence. > > I asked on stackoverflow and biostar.stackexchange.com for some input, > and the answers pointed me towards enums and a lookup table using > these. So I sat down and wrote that (that LUT took me quite some time, > I hope I did not make errors in there) and made a small class to > quickly get to the result. > > I post the code as cookbook page for future reference, possible > inclusion of the code into the library and of course, feedback. > > http://biojava.org/wiki/BioJava:CookBook:Core:SequenceCompare > > 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
