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?