Question: How an alignment with multiple HSPs is evaluated in blastn, blastp?
gravatar for sajal
21 months ago by
sajal0 wrote:

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?

ADD COMMENTlink modified 20 months ago by Jean-Karim Heriche18k • written 21 months ago by sajal0
gravatar for Jean-Karim Heriche
20 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

Yes, it's based on the sum statistics. The significance of an alignment is derived from the sum of the selected HSPs scores (see this Karlin & Altschul paper for the ungapped version, this was also shown to work for gapped alignments)

ADD COMMENTlink written 20 months ago by Jean-Karim Heriche18k

Jean-Karim: Thanks! I came across this paper a while ago and was trying to find this in the blast code with no success. So, release note of BLAST+ 2.2.29: January 3, 2014 says:

"Ungapped BLAST no longer uses sum statistics by default. Recover old behavior with -sum_statistics ˆag."

I am not sure if it's in use for gapped alignment though.

ADD REPLYlink written 20 months ago by sajal0
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