[GUSDEV] using VirtualSequence for scaffolding assemblies (not EST assemblies!)

[Aaron J. M. <am...@pc...>]

We're using (perhaps incorrectly) the VirtualSequence and  
SequencePiece tables to represent chromosomal assemblies of scaffolds  
(stored in ExternalNASequence).

1) VirtualSequence has a required sequence_version attribute - what  
is this for?  Is this redundant to external_database_release_id?

2) VirtualSequence has a clob for storing the assembled sequence (I  
suspect), but the Perl object layer doesn't use this slot, instead  
rebuilding the sequence from the sequence pieces.  Am I correct in  
this usage, or should I not, in fact, be storing the assembled  
sequence in VirtualSequence?

Thanks,

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205
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postal: Penn Genomics Institute
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