I have my own database of sequences stored in MySQL. I convert this database into a blastable format using formatdb, code below:
formatdb -p T -i db.fasta
I then do the same with the query sequence and the blast the query against my database using the code below:
blastall -d db.fasta -i query.fasta -p blastn -m 8 -e 0.01 -o output.blast
In the output.blast file i get something like this:
1_0 100.00 910 0 0 1 910 4 913 0.0 1438
I queried the database with a sequence i knew that was already in the database (NCBI ID= AAK92094). Where the value "1_0" is i would like it to the NCBI ID number which i have stored in the database fasta file.
The format of my db.fasta file looks like this before i convert it to a blastable format.
AAK92094
MNM........to the end of the sequence
NP_882282
MRCT.......to the end of the seqeunce
Any idea how i do it?
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