There's also a good deal of alignment quality checking, thresholding, and scoring the overlapping region that is both necessary and but maybe not all that straightforward. I suggest that you check out the PANDAseq paper, which describes their algorithm.
http://dx.doi.org/10.1186/1471-2105-13-31 Andreas is correct - the basic building blocks are already there. Chris On Apr 24, 2013, at 10:48 AM, Andreas Prlic <andr...@sdsc.edu> wrote: > It sounds like as all you need is to get the reverse complement of one of > your sequences and then you do a local alignment. Both should be possible > with BioJava... > > Andreas > > > On Wed, Apr 24, 2013 at 7:29 AM, Khalil El Mazouari > <khalil.elmazou...@gmail.com> wrote: > Hi Chris, > > my application is deployed as war file. I am trying to avoid, as much as > possible, to shell out to other none java programs... for maintainability > reasons. > > I don't think I need a 'full' genome assembly tools (eg velvet ...), it's > overkill for my case: cloned gene is sequenced on both directions. Normally > one strand is sufficient. If the sequence quality is not good enough, the 2 > strands are used to get the full length gene. There is always a large overlap > between the 2 strand sequence. > I can QC the full length gene. > > Best > > khalil > > > > > > > > ----- > > 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. > > > > On 24 Apr 2013, at 16:04, Chris Friedline wrote: > > > Khalil, > > > > Why not just shell out to programs designed for this purpose and pull in > > the results? We are in the process of publishing a paper which uses > > PANDAseq to assemble overlapping PE reads. The latest version of mothur > > also does this. > > > > www.mothur.org > > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler > > > > PANDAseq is particularly nice in this case, because you could read right > > from stderr and stdout streams. It's also wicked fast. > > > > Chris > > > > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari > > <khalil.elmazou...@gmail.com> wrote: > > > >> Hi, > >> > >> It's not a global sequence alignment nor genome assembly. It's just a DNA > >> fragment sequenced from both ends with an overlapping region. I want to > >> assemble the 2 reads in order to get the full length sequence. This > >> assembly is a part of a complex analysis process that uses biojava. > >> I agree, there a lot of simple option how to achieve this. But I need > >> somthing in java/biojava. > >> > >> Best > >> > >> khalil > >> > >> > >> > >> > >> ----- > >> > >> 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. > >> > >> > >> > >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote: > >> > >>> If you just have two contiguous sequences to align, you should just use a > >>> global sequence alignment. See > >>> http://biojava.org/wiki/BioJava:CookBook3:PSA for 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 (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 > > > > > > > > > > > _______________________________________________ > 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
