From hlapp at gmx.net  Tue Dec 19 10:43:19 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 19 Dec 2006 10:43:19 -0500
Subject: [BioSQL-l] Question about biosql
In-Reply-To: <1166184005.8456.1.camel@localhost.localdomain>
References: <1166184005.8456.1.camel@localhost.localdomain>
Message-ID: <011A0B62-4807-4212-A5D1-BFC327F8A028@gmx.net>

Hello Virginia,

blast output is essentially a list of similarity pairs, i.e., paired  
feature objects (query and hit), which can be stored perfectly well  
in Biosql (using the seqfeature and feature_relationship tables).

The other question is how well the different Bio* languages readily  
support this through their language bindings. Bioperl-db, the  
language binding for bioperl, right now does not store feature  
hierarchies, unfortunately. I can't speak for the other toolkits,  
though, and of course if you planned to store them through custom  
code anyway then this won't matter to you.

	-hilmar

On Dec 15, 2006, at 7:00 AM, Virginia Gonzalez wrote:

>
> Hello,
>
> Do you plan to store blast output in biosql? Is there any  
> documentation
> about the objects that biosql will store?
> Thanks.
>
>
> Virginia Gonzalez, PhD student.
> Unidad de Fisicoqu?mica
> Centro de Estudios e Investigaciones
> Universidad Nacional de Quilmes
> Roque Saenz Pe?a 352
> B1876BXD Bernal
> Buenos Aires - Argentina
> te ++54 011 43657100 int 135
>
>


-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From hlapp at gmx.net  Tue Dec 19 15:43:19 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 19 Dec 2006 10:43:19 -0500
Subject: [BioSQL-l] Question about biosql
In-Reply-To: <1166184005.8456.1.camel@localhost.localdomain>
References: <1166184005.8456.1.camel@localhost.localdomain>
Message-ID: <011A0B62-4807-4212-A5D1-BFC327F8A028@gmx.net>

Hello Virginia,

blast output is essentially a list of similarity pairs, i.e., paired  
feature objects (query and hit), which can be stored perfectly well  
in Biosql (using the seqfeature and feature_relationship tables).

The other question is how well the different Bio* languages readily  
support this through their language bindings. Bioperl-db, the  
language binding for bioperl, right now does not store feature  
hierarchies, unfortunately. I can't speak for the other toolkits,  
though, and of course if you planned to store them through custom  
code anyway then this won't matter to you.

	-hilmar

On Dec 15, 2006, at 7:00 AM, Virginia Gonzalez wrote:

>
> Hello,
>
> Do you plan to store blast output in biosql? Is there any  
> documentation
> about the objects that biosql will store?
> Thanks.
>
>
> Virginia Gonzalez, PhD student.
> Unidad de Fisicoqu?mica
> Centro de Estudios e Investigaciones
> Universidad Nacional de Quilmes
> Roque Saenz Pe?a 352
> B1876BXD Bernal
> Buenos Aires - Argentina
> te ++54 011 43657100 int 135
>
>


-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================