Question: Ncbi Blast Output Missing Subject Name
gravatar for Razzmataz
7.3 years ago by
Saint Louis, MO
Razzmataz30 wrote:

I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for the subject for the hits I get.

These are the blast commands I am using:

blastx -subject blastdb/nr.pal -query 0.fa -out 0.blast.out
blastx -db blastdb/nr.pal -query 0.fa -out 0.blast.out

I have ended up with output like this:

BLASTX 2.2.25+

Query= 5350 787 3793



 Score = 13.9 bits (24),  Expect = 1.9
 Identities = 4/6 (67%), Positives = 6/6 (100%), Gaps = 0/6 (0%)
 Frame = +1

Query  763  IPLQSF  780
Sbjct  85   MPLESF  90

 Score = 11.9 bits (19),  Expect = 7.3
 Identities = 4/9 (45%), Positives = 6/9 (67%), Gaps = 0/9 (0%)
 Frame = +1

Query  463  PENFV*SSP  489
            P++   SSP
Sbjct  43   PDBSWISSP  51

As you can see the Subject= is empty in these results.

I have tried changing the output to blastxml, I've tried downloading the fasta file for NR, and formatting that into a blast database, and I still end up with the same situation. My question, is there some option I'm missing from blast that omits the subject, or a different way to specify the blastdb?

I'm running NCBI blast 2.2.25+, and using the NR file and databases from NCBI.
Thanks in advance!

ncbi blast • 2.0k views
ADD COMMENTlink written 7.3 years ago by Razzmataz30

type ls in your blastdb directory, what is there?

ADD REPLYlink written 7.2 years ago by Michael Dondrup46k
gravatar for Damian Kao
7.3 years ago by
Damian Kao15k
Damian Kao15k wrote:

Is there a reason why you are using "nr.pal" as your database instead of just "nr"? Did you rename your nr database files? Try running:

blastx -db blastdb/nr -query 0.fa -out 0.blast.out
ADD COMMENTlink written 7.3 years ago by Damian Kao15k

I had been getting some errors when I tried that, something about "no database nr present", so I put in the full path to the database alias file. I'll try this again...

ADD REPLYlink written 7.3 years ago by Razzmataz30

actually you might be missing some files there, this error message is not good.

ADD REPLYlink written 7.2 years ago by Michael Dondrup46k

I've actually been able to get this to run without any problems now, similar to the query you have above. Not sure what I did wrong, but I'll chalk it up to only having used WU-BLAST up until recently... Thanks for the help!

ADD REPLYlink written 7.2 years ago by Razzmataz30
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