When blastn finishes searching, it reports many alignments (hits or query-sequence match), many of these alignments consist of many hsps. So, when it picks the top alignments, how does it evaluate the alignments's score?
I know how each HSP is scored and how the score is used to compute evalue. But, how these individual HSPs contribute to the alignment's score? If there is no idea of score for an alignment, then how does blast decide which alignments to keep and report?
I was going with the idea that every alignment is judged with it's highest scoring HSP (or lowest evalue HSP). But when I do split-database query, I found some alignment with a pretty high scoring HSP does not get picked by the search when run on the whole database. Is there any sum-statistics in play when evaluating alignments?