Algorithms on Sequences

Validation of a local alignment (2)
• E is an indication of the degree of surprise one gets
with the observed score : the highest it is, the least
significant is the score.
• A reasonable value of E is between 0.1 et 0.001
Biologists use generally 10 -4
• Blast default searches until 10
• One generally gives score results standardized with
respect to parameters K and λ :
S ' are called « bit scores »
s − ln K
S′
=
λ
Probability : P-value
ln 2
• The random number of HSP with a score ≥ s follows a
Poisson’s law, i.e. the probability to find exactly k HSP with a
score ≥ s is
e k E −
where E is the expected number of HSP previously defined.
• The p-value P associated to score s is the probability to find
at least one HSP :
−E
P
k! E
= 1−
For instance, if the expected number of HSP with a score ≥ s
is 3, the probability to find at least 1 HSP is 0,95.
e