[Bioperl-l] Blast Searching with Bioperl

[Phillip Lord]

Apologise for a beginners question when you're probably all busy with
the 1.0 release.....


I'm trying to find the best way of performing a blast search with
bioperl. I've tried using the Bio::Tools::Run::RemoteBlast code, using
code culled from the remote-blast.pl script with a little
success. This seems to work reasonably well, at least until the US
wakes up, and then it starts to take for ever.

We have on site a reasonable fast machine with lots of databases
installed, and I'd quite like to use this. But I can't run all of my
perl on this machine, because I need access to other software only
installed locally. I couldn't see anyway to get the "local blast"
bioperl options to work by ssh'ing to another machine.

I've tried setting up the "www server" software from NCBI, and then
accessing this through the RemoteBlast, which I presumed (well
hopefully guessed) was what NCBI were using. I noticed that
RemoteBlast contains the NCBI URL hardcoded, which didn't bode
well. I thought I would try this anyway, but it doesn't appear to
work...I'm getting an error reported from the libwww software. 

The question then is this:- is it possible to use the RemoteBlast
class on something other than the NCBI site? Is there a better way of
performing BLAST not on the machine running the perl, which I have (or
can get) ssh, or similar access to. Or would I be better of waiting
until Bill Gates has invented networking computing, and given it the
world like the philanthropist that he is. 

Phil