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.