[Bioperl-l] storing and retrieving partial sequences

[Jonathan Epstein]

Hi,

Does anyone have a good BioPerl or ACEDB way to handle storing and retrieval of partial sequences?

The idea is that, say, I might have bp 50001-100000 of a particular sequence which is 500kb long.  I want to cache this local result, since obtaining the other sequence data may be computationally very complex and may even require manual intervention.  So, if subsequently there is a query for bp 56000-60000 I want to retrieve the data immediately from the local cache.  If there is a query for bp 40000--60000 I want to retrieve the cached portion of the data, and set in motion whatever is needed to obtain the missing data.

For now we are starting a home-grown mySQL solution, but I really prefer to use a solution which is BioPerl-based or at least BioPerl-like.

Can anyone suggest how we might hook into Bio::DB or Bio::Seq or ... ?

Thanks,

- Jonathan