BLAST COMPARISON

Richard E. Showalter rich at vaxkiller.agi.org
Tue Sep 3 11:05:33 EST 1991


In article <Aug.28.10.25.16.1991.25498 at genbank.bio.net>  
kristoff at genbank.bio.net (David Kristofferson) writes:
> Thanks, Win.  I hope others will share their BLAST and FASTA
> experiences since it should prove to be of general value.
> 
> 				Sincerely,
> 
> 				Dave Kristofferson
> 				GenBank Manager
> 
> 				kristoff at genbank.bio.net
I would love to relay my experience with a blast comparison but I am having a  
problem with the BLASTP, BLASTX, BLAST3 programs.  I was able to compile the  
set of BLAST programs on a NeXT  workstation.  I converted the Genabank and PIR  
databases into the correct formats for BLAST. (by the way keeping two different  
copies of these databases to run various software products is a real pain in  
the disk space)  BLASTN is very fast. ~2 seconds to search the gbbct subset  
with a 2.2kb DNA sequence and it found all three DNA patterns which I had  
identified previously with the FASTA set of programs.  I can not get the BLASTP  
program to work I keep getting an error that says "too many HSP hits raise  
MAX_HSP and recompile"  I have raised MAX_HSP to 5000 from 500 and all it does  
is cause the program to go into the ozone grabing all my swap space until it is  
killed.  Any help would be appreciated.  Also if these programs are made  
available on a server machine, our group would be very interested in using the  
service.  I have a few scripts which use the FASTA at genbank.bio.net and this  
is a nice feature for my users.
--
*********************************************************************
					    |  Rich Showalter
"Hey, hey, hey, hey, it was the DNA,        |  SysAdmin
hey, hey, hey, hey, that made me this way." |  Agouron Institute
(Queen) 				    |  rich at vaxkiller.agi.org
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