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

[Barry Moore]

Richard-

Thanks much for the help, and the solution.  I use this program to help 
look for trans-frame proteins - that is proteins that require a 
frameshift for expression.  With that in mind, this program BLASTs the 
translation of every ORF, and plots that ORF in shades of yellow 
(representing it's e-value) on a 3 frame plot of the transcript.  It may 
be that blastx would work, and I could just map the location of 
significant HSPs onto my plot.  When I started working on the program I 
tried translating the entire transcript (stops and all) in 3 frames, and 
BLASTing the 3 frames.  I noticed that I wouldn't get HSPs to some small 
ORFs that I could get by BLASTing those ORFs individually.  Because of 
that and because at the time it seemed simpler to keep track of and plot 
the results if each ORF was handled separately, I went that way.  In 
retrospect now that I've seen how long it can take to BLAST 26 small 
ORFs I think it would be a good idea to go back and check more carefully 
if I can achieve the same results with blastx.  It may be that by 
tweaking the parameters to BLAST, I can see hits to all the small ORFs 
on the transcript.  Thanks again for your help, and for the suggestions.

Barry

Richard Adams wrote:

> 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
>