Hi, I will combine local alignment + http://biojava.org/wiki/BioJava:CookBook:Core:SequenceCompare . I think this will do the job.
Thanks for your help 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 16:58, Chris Friedline wrote: > 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
