[Bioperl-l] Comparing DB_FILE and SDBM

[Mike Muratet]

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
intensive.

> > 
> > 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?

Thanks

Mike