Re: Multiple Sequence Alignment - Limits?

Hannes–

There should not be a limit on the number of sequences, nor should you be
running into a memory problem. The FastaParser should be able to read
thousands of sequences, since it is used for genome FASTA files as well as
multiple alignments. My guess would be either a malformed FASTA file
(perhaps a problem with line endings?), or else a problem with the code to
generate the MultipleAlignment. Can you post some code snippets?

-Spencer

On Tue, Oct 18, 2011 at 21:36, Hannes Brandstätter-Müller <
[email protected]> wrote:

> Hi Andreas,
>
> I will try that later today if that makes any difference; I ran a
> larger alignment batch overnight, and I noticed that this limit seems
> to have been a coincidence; HOWEVER, the aligned sequences are always
> not as many as the input sequences, is this caused by memory
> constraints or how can I influence that?
>
> Hannes
>
> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <[email protected]> wrote:
> > Hi Hannes,
> >
> > did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> >
> > Andreas
> >
> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandstätter-Müller
> > <[email protected]> wrote:
> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandstätter-Müller
> >> <[email protected]> wrote:
> >>> Hi again!
> >>>
> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
> >>> that there seems to be a limit of 132 Sequences that are present in
> >>> the final alignment - is this some kind of hardcoded limit, or can I
> >>> work around that somehow?
> >>>
> >>> Hannes
> >>>
> >>
> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
> >> fasta format. Is there a way to work around that limit?
> >>
> >> Hannes
> >>
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