Question: OID not found
0
gravatar for arashrostamiazar
4.0 years ago by
arashrostamiazar0 wrote:

Hello

I am running standalone BLAST version 2.2.31 locally on my computer.I wanted to do BLASTx against Nr database. For this I downloaded the database and configured the system according to the mannual.

but it is giving this error: "OID not found"

Can anybody tell me what is wrong with the commands?
thanks

blastdbcmd blast blastx oid • 2.1k views
ADD COMMENTlink modified 4.0 years ago by Ahill1.6k • written 4.0 years ago by arashrostamiazar0
2
gravatar for Ahill
4.0 years ago by
Ahill1.6k
United States
Ahill1.6k wrote:

The "blastdbcmd" will not run blastx.  For that, use the blastx command.  I'm not sure what your goal is but do you really want to run blastx, or blastp of the corresponding protein (NP_000113.1) against nr?

From the accession you are entering, it looks like you may be using the wrong database.  This is RefSeq human mRNA accession, which seems very unlikely to be present in the standard nr protein database.  Table 3b here shows pre-formatted nucleotide databases that include human NM accessions, like human_genomic_transcript.tar.gz.

To confirm what OIDs are present in your nr database, you can use the blastdbcmd -entry all -outfmt '%o' options.

 

ADD COMMENTlink written 4.0 years ago by Ahill1.6k

I want to run blastx. first i tried by another accessions. but results was the same. this accession (nm) was in the manual (of course for running blastn and against RefSeq database) and i just tested it.

how i must use bast x command? (what is its command?)

when i entered a protein accession, it works. but at the next command for runnig blastx, definitely it will be incorrect.

ADD REPLYlink written 4.0 years ago by arashrostamiazar0

The blastx error message suggests your test_query.txt file is not a valid FASTA format nucleotide sequence.  BLASTX takes a nucleotide query as input, not a protein sequence.  Does test_query.txt contain the nucleotide sequence for NM_000122 in valid FASTA format?   

One way to test your query is to use NCBI's web-based blastx here, and paste your query sequence into that tool.  

 

ADD REPLYlink written 4.0 years ago by Ahill1.6k

Yes. It does. it's format is valid.

About protein sequence, I just wanted to know can this program take sequences from nr database, or not.

I pasted my sequence (even sequences) into NCBI's web-based blastx and i tested it. it had no error.

but when i tried in command prompt, it gave these errors.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by arashrostamiazar0
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