This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to run BLAST against the targets and then parse the output file (looking at every hit one at a time) and then finding the best hit.
My question is, is there any other way to do this? For example, already getting sorted output (according to bit score) and then retrieve the first hit?
EDIT (added information):
To make it clear, I want to search 1 (or more) sequences with a custom database using local NCBI BLAST (nucleotide vs nucleotide). I donot want to use e-value as criterion as the length of alignment is important. Thats why I would like to use bit score. As per Pierre's link what I need is -v. Thanks again for comments.
Any suggestions are welcome.