Re: DNA assembly

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 <
[email protected]> 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
>
>
>
>
>
>
>
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> 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 <
> [email protected]> 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
> >>
> >>
> >>
> >>
> >> -----
> >>
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> >>
> >>
> >>
> >> 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 <
> [email protected]> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there
> something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
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