Hello All,
I need some help in optimizing my blastall query. I have a file of 10000 genes, and i wanted to blast them against themselves. So, i created blast db to perform blastall. But i dont want the genes that map to themselves. I would like to get second best hit from the results. Can i do this in blastall using some parameters or do i need to write a perl script for this?
That is the query i uses and it brings out blast results in tabular format..
please help me if u know optimizing blast queries.
Thank you all
I need some help in optimizing my blastall query. I have a file of 10000 genes, and i wanted to blast them against themselves. So, i created blast db to perform blastall. But i dont want the genes that map to themselves. I would like to get second best hit from the results. Can i do this in blastall using some parameters or do i need to write a perl script for this?
Code:
blastall -p blastn -m 9 -d testgenesdb -i test.fasta -o outputtest.QUERY
please help me if u know optimizing blast queries.
Thank you all
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