Blast Report: Expect(2) = number instead of Expect = number, what does it means?

Question

[dssouzadan]

Hi all, in the sample below is shown two alignments with Expect and Expect(2) report:

Score =  248 bits (129), Expect = 1e-63
  Identities = 213/263 (80%), Gaps = 34/263 (12%)
  Strand = Plus / Plus

  Query: 161 atatcaccacgtcaaaggtgactccaactcca---ccactccattttgttcagataatgc 217
             |||||||||||||||||||||||||||||  |     | |   || ||||||||||||||
  Sbjct: 481 atatcaccacgtcaaaggtgactccaact-tattgatagtgttttatgttcagataatgc 539

  Query: 218 ccgatgatcatgtcatgcagctccaccgattgtgagaacgacagcgacttccgtcccagc 277
             |||||||   ||||||||||||||||||||| || |            ||||||||||||
  Sbjct: 540 ccgatgactttgtcatgcagctccaccgattttg-g------------ttccgtcccagc 586

  Query: 278 c-gtgcc--aggtgctgcctcagattcaggttatgccgctcaattcgctgcgtatatcgc 334
             |  || |  | ||||||||||||||||||||||||||||||||||||||| |||||||||
  Sbjct: 587 caatgacgta-gtgctgcctcagattcaggttatgccgctcaattcgctgggtatatcgc 645

  Query: 335 ttgctgattacgtgcagctttcccttcaggcggga------------ccagccatccgtc 382
             |||||||||||||||||||||||||||||||||||            |||||||||||||
  Sbjct: 646 ttgctgattacgtgcagctttcccttcaggcgggattcatacagcggccagccatccgtc 705

  Query: 383 ctccatatc-accacgtcaaagg 404
              |||||||| |||||||||||||
  Sbjct: 706 atccatatcaaccacgtcaaagg 728

Score = 80.5 bits (197), Expect(2) = 3e-17
Identities = 35/37 (94%), Positives = 36/37 (97%)
Frame = +2

Query: 2   EDKDGDWMLVGDVPWEMFVESCKRLRIMKGKEAVGXG 112
           EDKDGDWMLVGDVPWEMFVESCKRLRIMKGKEA+G G
Sbjct: 194 EDKDGDWMLVGDVPWEMFVESCKRLRIMKGKEAIGLG 230

The calculation of the Expect value for the first sequence is good-old E=(Kmn*exp(-Lam*S))/H For the second, I'm not really sure at all what Expect(2) means. It doesn't seem to relate to the E=(Kmn*exp(-Lam*S))/H equation at all.

Answer 1

[David W]

The expect(n) values are calculated when there are multiple HSPs in different frames, and come from the sum of statistics from n HSPs. There are a few more details here

[dssouzadan]

Thanks for the answer. Now it makes sense!