[Bioperl-l] Remote BLAST returning lots of 500 time out errors

[Richard Adams]

Hi Barry,
I've changed the RemoteBlast module so that it no longer uses temporary 
files - version 1.19 in CVS.
This is just a temporary solution as I'm not sure why making temporary 
files is causing this problem just now.
But it should work OK all being in memory, unless you are making vast 
Blast outqput  files.
You don't have to change your script at all. It now appears to be run OK.

Just curious, why don't you just submit the RNA sequence and use  
Blastx? This translates all your sequences and means you only have to submit
1/6th as many sequences to the server..
Cheers
Richard

-- 
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk