If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSAfor how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool<http://en.wikipedia.org/wiki/Sequence_assembly>(eg Velvet). -Spencer On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari < khalil.elmazou...@gmail.com> wrote: > Hi, > > I would like to assemble 2 overlapping DNA sequences. Is there something > in biojava that may help in this task? > > Thanks > > > > > ----- > > Confidentiality Notice: This e-mail and any files transmitted with it are > private and confidential and are solely for the use of the addressee. It > may contain material which is legally privileged. If you are not the > addressee or the person responsible for delivering to the addressee, please > notify that you have received this e-mail in error and that any use of it > is strictly prohibited. It would be helpful if you could notify the author > by replying to it. > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l