[Bioperl-l] Comparing DB_FILE and SDBM

Mike Muratet muratem at eng.uah.edu
Fri Aug 13 13:38:47 EDT 2004

On Thu, 12 Aug 2004, Josh Lauricha wrote:

> On Thu 08/12/04 13:44, Mike Muratet wrote:
> > Greetings
> > 
> > I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
> > on the latest version of the files from the Genbank primate division using
> > a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the
> Wow, now thats a machine in desprate need of a memory upgrade.

Well, yes. But it's all I've got.
> How loaded was that machine? (I'm assuming just the tests.)

I had some X sessions going to other (larger ;-) ) machines, but nothing

> > 
> > A negligible difference. Has anyone tried to compare the libraries (or
> > knows where someone has?)
> I have a feeling that perl yeilds its timeslice for whatever reason when
> switching from a library to perl-code, making libraries that do a lot of
> function calls (such as XML parser and DBs) very slow in terms of
> latency.
> Can anyone confirm or deny this?

If anyone has any experience(s) to relate regarding the indexing of big
portions of Genbank, I'd like to hear how they did it. Should it really
take days?



More information about the Bioperl-l mailing list