[Bioperl-l] StandAloneBlast.pm question

[Peter Schattner]

Andrew Emerson wrote:

> In some cases the system call is in a loop and called many tens of
> thousands of times, resulting in long execution times as a result of
> repeatedly loading the nucleotide database by Blast.
> Can  StandAloneBlast.pm be of any use or does it just effectively work like
> the system call?

StandAloneBlast.pm is effectively just a system call

> Will I be forced to get my hands dirty
> with C and call the Blast functions directly?
>

Probably you will.  If you come up with a nice way of doing this that
maintains a perl interface, you might consider contributing it to bioperl
since it would be an improvement :-)

Regards

Peter Schattner