Entering edit mode
4.6 years ago
To our surprise, we have recently discovered that this intuition is incorrect. Instead, BLAST returns the first N hits that exceed the specified E-value threshold, which may or may not be the highest scoring N hits. The invocation using the parameter "-max_target_seqs 1" simply returns the first good hit found in the database, not the best hit as one would assume.
My bad for not noticing the previous posts. Anyway, I think this issue deserves a lot of visibility. Like one of those previous posts could be a sticky until NCBI does something about it..
+1 for the "deserves a lot of visibility" !