[DAS2] Fwd: Accelerating interval queries

[Allen Day]

And again, from my ucla.edu address :)

-Allen

---------- Forwarded message ----------
From: Allen Day <allenday at gmail.com>
Date: Jun 25, 2007 11:41 PM
Subject: Re: [DAS2] Accelerating interval queries
To: Ann Loraine <aloraine at gmail.com>
Cc: Steve Chervitz <Steve_Chervitz at affymetrix.com>, DAS/2 Discussion
<das2 at lists.open-bio.org>, Scott Cain <cain.cshl at gmail.com>


I see Alex occasionally in my building, I'll ask him next time I see
him.  Without looking closely at the data structure in the paper, I am
thinking we may be able to implement this indexing scheme with the
PostgreSQL GiST mechanism for new index strategies.

-Allen

On 6/25/07, Ann Loraine <aloraine at gmail.com> wrote:
> Interesting!
>
> This is definitely needed.
>
> How do we incorporate this into our own schema?
>
> On 6/25/07, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
> > Of potential interest to genome DAS server implementers:
> >
> > Nested Containment List (NCList): a new algorithm for accelerating interval
> > query of genome alignment and interval databases
> >
> > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386
> >
> > Any comments on this approach or comparison with other methods?
> >
> > Steve
> >
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das2
> >
>
>
> --
> Ann Loraine
> Assistant Professor
> University of Alabama at Birmingham
> http://www.transvar.org
> 205-996-4155
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>


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