Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?
I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with partial sequence of one of the sequences in SETREF as a query (SET_Q : testQ.fa). But the result shows No Hit.
This is the SET_REF:
>Glyma0021s00410.1|PACid:16242639
ATGGCTCGTAAGAAGCAAA[...]
>Glyma0021s00460.1|PACid:16242642
ATGGAACAAAATCTGTACA[...]
And this is the SET_Q:
>seq1
ATGGCTCGTAAGAA[...]
seq1 in SETQ is just the first line in the first sequence in SETREF.
I applied makeblastdb to SET_REF:
makeblastdb -in testDB.fa -title "test DB"
Then applied blastx:
blastx -db testDB.fa -out testQ.blastx -query testQ.fa
But then there is No Hit for the query sequence, did I missed out something? Why the query sequence is an exactly same sub-sequence as the reference but returned no alignment? Thanks a lot in advanced.
For BLASTx you need a PROTEIN database. To this DB you can only do a BLASTn. Or do I misunderstand?
An alternative for using the DB as nt would be to use tblastx. Translated blast query against a translated DB.
Nothing to add here. Except, maybe: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide#blastx
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written
by
Michael Schubert
Thanks ALchEmiXt, I got it now. I was confussed with the makeblastdb option -dbtype. It can take 'nucl' (nucleotide) or 'prot' (protein)[default] as arguments. I misunderstand that it will translate the input fasta sequence and make the output as a protein database. Then in this case, I think I need to use '-dbtype nucl' as an option for the makeblastdb, don't I?
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