question about delta blast warning

Kennels · 04-28-2013, 11:22 PM

Hi,

I'm running deltablast with the rpsdb database as CDD v3.1 downloaded off ncbi (I ran makeprofiledb on the raw .pssm's to make applicable for deltablast). I am running into warnings like this:

##
Warning: lcl|Query_9517: Warning: Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics
##

It is not for all queries.

This is the first time I'm running delta blast, so I'm wondering if this is something to worry about when interpreting the output. Does this just mean there wasn't any conserved domains detected for the particular query?

Any comments greatly appreciated. Thanks.

klager · 07-04-2013, 12:36 AM

Yes, the warning comes just because no CDD domain was found. And it's possible to download a cdd_delta.tar.gz from NCBI Blast ftp site, so you don't have to index CDD your self.

rhinoceros · 07-04-2013, 02:31 AM

Did you build your db as suggested in this document?

klager · 07-08-2013, 09:22 AM

As described in the BLAST 2.26+ Release, there's a special version of the CDD database (cdd_delta) available from the BLAST db directory on the FTP site:

http://www.ncbi.nlm.nih.gov/books/NBK92578/
ftp://ftp.ncbi.nih.gov/blast/db/

No need to build a CDD db

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04-28-2013, 11:22 PM	#1
Kennels Senior Member Location: Sydney Join Date: Feb 2011 Posts: 149	question about delta blast warning Hi, I'm running deltablast with the rpsdb database as CDD v3.1 downloaded off ncbi (I ran makeprofiledb on the raw .pssm's to make applicable for deltablast). I am running into warnings like this: ## Warning: lcl\|Query_9517: Warning: Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics ## It is not for all queries. This is the first time I'm running delta blast, so I'm wondering if this is something to worry about when interpreting the output. Does this just mean there wasn't any conserved domains detected for the particular query? Any comments greatly appreciated. Thanks. Last edited by Kennels; 04-29-2013 at 12:14 AM.

07-04-2013, 12:36 AM	#2
klager Junior Member Location: Finland Join Date: Oct 2012 Posts: 2	Yes, the warning comes just because no CDD domain was found. And it's possible to download a cdd_delta.tar.gz from NCBI Blast ftp site, so you don't have to index CDD your self.

07-04-2013, 02:31 AM	#3
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	Did you build your db as suggested in this document?

07-08-2013, 09:22 AM	#4
klager Junior Member Location: Finland Join Date: Oct 2012 Posts: 2	As described in the BLAST 2.26+ Release, there's a special version of the CDD database (cdd_delta) available from the BLAST db directory on the FTP site: http://www.ncbi.nlm.nih.gov/books/NBK92578/ ftp://ftp.ncbi.nih.gov/blast/db/ No need to build a CDD db