[BioSQL-l] Gene Cluster

[Hilmar Lapp]

Hi Raoul,

I have done this in the past using the bioentry_relationship table.  
This assumes that the "genes" (or, more generally, the members of the  
cluster) are bioentries, not seqfeatures. If you use BioPerl to read/ 
process/represent the clusters, and your are using the Bio::ClusterI  
interface for that (any of the Bio::Cluster::* modules, for example),  
the Bioperl-db should support mapping those to the schema.

Obviously, you can do the same for seqfeatures using  
feature_relationship.

	-hilmar

On Jan 18, 2008, at 5:11 AM, Raoul Jean Pierre Bonnal wrote:

> Hi all,
> I need to represent Gene Clusters using BioSQL' schema.
>
> Actually, I don't know if it's better to add a feature which contains
> all the genes involved or add a qualifier to genes, and cds.
>
> Feature Keys eligible are misc_feature or source. In this case I  
> need to
> populate Seqfeature_Relationship to keep track of what gene/CDS is  
> part
> of which cluster.
> Second option is adding a qualifier (/note?) to every gene/cds.
>
>
> --
> Ra
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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