[BioSQL-l] Genbank loading time

[Peter]

On Tue, Jan 27, 2009 at 10:57 PM, Richard Holland wrote:
>
> As for BioPerl/BioPython/etc. I expect their respective project authors
> will respond to this thread accordingly with the figures from their own
> domains!

I can tell you importing GenBank files into BioSQL with Biopython is
faster than BioPerl, sometimes several times faster, but this will
depend on the nature of the files (e.g. genomes versus ESTs).
http://lists.open-bio.org/pipermail/biosql-l/2008-August/001320.html
http://lists.open-bio.org/pipermail/biopython-dev/2008-April/003625.html

I don't have any BioJava comparison figures.  In any case, as Richard
points out, there will be slight differences in the different Bio*
tools how exactly how the data is parsed and stored.

I've never tries to import the whole of GenBank, so I don't have any
numbers for you there.

Peter
(Biopython)