Makeblastdb And Blastx
1
1
Entering edit mode
12.4 years ago
Ken ▴ 160

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.

blast makeblastdb short • 6.6k views
ADD COMMENT
5
Entering edit mode
12.4 years ago
ALchEmiXt ★ 1.9k

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.

ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

Yes you can only FORMAT a BLAST DB of iets own content. The algorithms can ANALYSE 6 frame translated versions for you. The blast+ suite of ncbi also lets you do this directly on input FASTA query AND FASTA DB sequences.

ADD REPLY
0
Entering edit mode

Thanks heaps!!!

ADD REPLY

Login before adding your answer.

Traffic: 1501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6