[Biojava-l] Biojava-l Digest, Vol 105, Issue 5

[Shakuntala Baichoo]

Does anyone know how to find codon usage from data in a genbank file or embl
file.

Thanks
Shakun

On Fri, Oct 7, 2011 at 8:00 PM, <biojava-l-request at lists.open-bio.org>wrote:

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> Today's Topics:
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>   1. Re: losing meta-info after multiple sequence alignment
>      (Spencer Bliven)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Oct 2011 11:29:06 -0700
> From: Spencer Bliven <sbliven at ucsd.edu>
> Subject: Re: [Biojava-l] losing meta-info after multiple sequence
>        alignment
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
>        Scooter Willis <HWillis at scripps.edu>
> Message-ID:
>        <CA+P6arkEx4RTGWo=HadaCX1v41FBv-CiPUudq7LLo+ooOCXR9Q at mail.gmail.com
> >
> Content-Type: text/plain; charset=UTF-8
>
> I think that 1-based indexing was chosen because that's what's used in
> genome databases like GenBank. Thus gene offsets from outside data sources
> can be used directly without subtracting 1. That said, almost every time I
> write code using sequences I get off-by-one errors, so I understand your
> frustration. We should definitely improve documentation so that every
> method
> that takes 1-based indexes are clearly marked.
>
> -Spencer
>
> On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
>
> > Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> > just ask the mailing list if things are unclear before I add stuff to
> > the wiki.
> >
> > One thing that bugged me just now, and since I can't find documentation
> on
> > it:
> >
> > Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> > un-java-like, especially since you just get an OutOfBoundsException,
> > and the range is not specified in the javadoc, or I could not find it
> > easily in the complex class hierarchy.
> >
> > Hannes
> >
> > 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > > Hannes
> > >
> > > As you can tell we need to improve the cookbook examples. Since you are
> > > going through that process would welcome any contributions you can
> make.
> > >
> > > Thanks
> > >
> > > Scooter
> > >
> > > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <
> biojava at hannes.oib.com
> > >
> > > wrote:
> > >
> > >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
> > >><biojava at hannes.oib.com> wrote:
> > >>> Hi again!
> > >>> What I ran into now is that most of the meta-information of a
> Sequence
> > >>> seems to get lost during the MSA step.
> > >>
> > >>Okay, that was something caused by following another cookbook script
> > >>(that, unfortunately, has absolutely no docs or comments) - I found
> > >>the getOriginalSequence() method, can work with that. Thanks!
> > >>
> > >>Hannes
> > >>
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> > >
> >
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> End of Biojava-l Digest, Vol 105, Issue 5
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