[Biojava-l] InstabilityIndex

[Chuan Hock Koh]

Hi Andreas and Steve,

Sorry for the slow response. Currently, I am in the midst of moving from
Singapore to Japan. Busy with settling into the new job, apartment hunting
etc..

So, what is the conclusion for the problem? Do let me know what you guys
like to be done, as clear as possible :)

I will code them whenever I can find time which I believe I should have
some at the end of this month.

Thanks,
Ah Fu


On Thu, Oct 11, 2012 at 11:17 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks, good comments, Steve.
>
> I agree we should make it a policy from now on to support 6
> non-standard letters for anything protein related... About your time
> comment - that's part of the idea of moving the development to git..
> Ideally,  it should be easier for everybody who is concerned to patch
> and share patches...
>
> Andreas
>
>
> On Tue, Oct 9, 2012 at 10:32 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > @Subrata, The class does not handle characters other than the standard
> 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the
> approximation.
> >
> > @Ah Fu, In the past we have used average values for B (D or N), J (L or
> I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O
> substitutions just map to the closest natural amino acid. It would be nice
> if real values existed for selenocysteine and pyrrolysine, but I haven't a
> clue if they do.
> >
> > @Andreas, I would suggest that a general policy that all protein
> sequence analyses support the 6 non-standard letter would be a good thing.
> A nice ideal, but who has the time? :)
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org [mailto:
> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
> > Sent: Monday, October 08, 2012 5:44 PM
> > To: subrata sinha
> > Cc: Chuan Hock Koh; biojava-l at biojava.org
> > Subject: Re: [Biojava-l] InstabilityIndex
> >
> > Hi Subrata,
> >
> > Please don't mail me directly, but send your questions to the list.
> > Chances are that somebody there can help you best.
> >
> > Ah Fu, do you have any thoughts on this?
> >
> > Thanks,
> >
> > Andreas
> >
> >
> >
> >
> > On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <
> subratasinha2006 at yahoo.co.in> wrote:
> >> Dear Sir,
> >>
> >> I was testing the getInstabilityIndex() method of
> >> org.biojava3.aaproperties.PeptideProperties class.
> >>
> >> I am trying to find InstabilityIndex for very short segment of
> >> peptide, as short as two. But I am getting some surprising result in
> >> negative.Then i found that the method perhaps giving -ve result for
> >> ambiguous characters. So how to handle a situation if my protein
> >> sequence contains ambiguous characters
> >>
> >> Input Sequence            Instability Index
> >>
> >> GTDG                      -13.725
> >> VDVR                      -30.075
> >>
> >> How i analyse the above situation.
> >>
> >> Kindly help me.
> >>
> >>
> >> With Regards
> >>
> >> Subrata Sinha
> >> Assistant Professor
> >> Centre for Bioinformatics Studies
> >> Dibrugarh University
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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