In my case, the sequences were all pre-aligned, but yes, that could be done first.
A question concerning consensus sequences: how do you handle gaps? N (as I understood it) does not allow a gap. Is there a way to encode a "might be gap here, or A or G"? Hannes On Thu, Dec 22, 2011 at 14:29, Andreas Prlic <[email protected]> wrote: > 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
