Question: Blast Report: Expect(2) = number instead of Expect = number, what does it means?
0
gravatar for dssouzadan
5.7 years ago by
dssouzadan30
Brazil
dssouzadan30 wrote:

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.

blast • 1.5k views
ADD COMMENTlink modified 5.7 years ago by David W4.7k • written 5.7 years ago by dssouzadan30
2
gravatar for David W
5.7 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

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

ADD COMMENTlink written 5.7 years ago by David W4.7k

Thanks for the answer. Now it makes sense!

ADD REPLYlink written 5.7 years ago by dssouzadan30
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