[Biojava-l] queries on biojava

[Andreas Prlic]

Hi Parinita,

Please don't send BioJava related questions to me directly, but to the
mailing list.

Probably your genome sequences are very long and require a lot of
memory? Try increasing your Java memory to the maximum available on
your computer with something like -Xmx4G .

If this does not help and your DNA sequences are too long, you might
have to use either shorter DNA sequences, or you use one of the
alignment algorithms that are available for the alignment of larger
genomes.  Eg. Mummer might be one of the options.

Andreas


On Sat, Oct 29, 2011 at 10:25 PM, parinita ujoodha
<pari_ujoodha at yahoo.com> wrote:
> Hello andreas,
>                     I am currently an undergraduate final year student on
> the computer science course at the university of Mauritius.  I am doing a
> project on a genome comparison tool and using java and biojava as
> programming tools.  I have certain queries and hope you can answer them.
> I have tried the MSA in the cookbook and it works fine but when I try to
> align genomes, the program crashes.
> I would sincerely like to know whether there is a way of  aligning genomes
> and displaying them in a pleasant interface
> I thank you in advance
>
> Regards
> Parinita
>
>
>