Question: E-value from blastp search output does not match computed value from the formula
gravatar for sajal
3.1 years ago by
sajal0 wrote:

So, I ran a blastp query online and downloaded the output file.

I fetched gap-open and gap-extend values (a = 11, b = 1), that gave alpha = 1.9, beta = -30 from BLOSUM62. Then I computed length adjustment by solving the fixed point equation (using blast_stat.c's routine). length adjustment, l = 129.

I picked one HSP with score S = 79 (< Hsp_score>79< /Hsp_score>).

I picked lambda, K, N, n from following section:

< Statistics>

  <  Statistics_db-num>466914</Statistics_db-num> : N
  < Statistics_db-len>175697176</Statistics_db-len> : n
  < Statistics_hsp-len>0</Statistics_hsp-len>
  < Statistics_eff-space>0</Statistics_eff-space>
  < Statistics_kappa>0.041</Statistics_kappa> : K
  < Statistics_lambda>0.267</Statistics_lambda> : lambda
  < Statistics_entropy>0.14</Statistics_entropy>

< /Statistics>

m = query length = 1286.

Then I computed evalue using this formula: evalue = K * (m - l) * (n - N*l) * e^(-lambda * S), and I get 3.7843. But, the output file gives me 3.35488. I tested for different hsps, I never get the same value as the output file.

Am I doing anything wrong, or the formula changed subtly? Am I reading m wrong; should m change depending on HSP length, but not the query length?

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by sajal0

The scoring method got changed in version 2.2.26. In stead of old length adjustment, an "improved finite score correction" method is used. "An improved finite size correction is now used for blastp/blastx/tblastn/rpsblast." (

The method is described in the paper titled, "New finite-size correction for local alignment score distributions". I am yet to find where in the code this actually happens.

ADD REPLYlink written 3.1 years ago by sajal0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1577 users visited in the last hour