Hi, I was blasting proteome of yeast against a large database of Archaea. Something is wrong with the results because I got too large P Identity for too much proteins. I assume that the problem is that blast scores small parts of the query sequence once it found an alignment to that, and therefore gives good scores even though most of the query sequence doesn't match. How can prevent blast from giving me small alignments? maybe setting the window_size parameter? or normalizing the bitScore with the query length? does hsps have to do something with that? Thanx soo much!