Bioperl: Bioperl sequence object

Ian Korf
Tue, 9 Jun 1998 10:08:47 -0500

I'm looking forward to a discussion of the Bioperl sequence object at ISMB. I
think a good way of starting this is by examining the sequence classes in use
use at the moment (eg. Genbank/EMBL, sequencing centers), and making sure our
model easily translates to theirs.

I'm not sure what level Tool and Feature really belong in Bio::GSC. As it is
now, a Feature doesn't know what Tool it belongs to, which is odd, but
reiterating that information for all Features is a lot of redundancy. But if
you look at a Genbank flatfile, there is no Tool, only a Features with Tool
information. I'm not wedded to the current implementation of Bio::GSC. Having
Tools one level up makes it simple to compare them to each other, but the
Bioperl sequence class need not be limited by such conveniences.

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