DIVERSIFYING SELECTION AND FUNCTIONAL CONSTRAINT
-
Upload
hammett-bentley -
Category
Documents
-
view
24 -
download
5
description
Transcript of DIVERSIFYING SELECTION AND FUNCTIONAL CONSTRAINT
DIVERSIFYING SELECTION AND FUNCTIONAL CONSTRAINT
ESTIMATING THE dN/dS RATIO FOR GENE SEQUENCES IN THE PRESENCE OF
RECOMBINATION
Danny Wilson18th August 2005
Example: CTT
C T T T TT TT T
C TC TC TC TC TC T
TAG
CAG
CAG
Phe Non-synonymous transition
Ile Non-synonymous transversion
Val Non-synonymous transversion
Ser Non-synonymous transition
Tyr Non-synonymous transversion
Cys Non-synonymous transversion
Phe Non-synonymous transition
Leu Synonymous transversion
Leu Synonymous transversion
Leucine
Example: CTT
C T T T TT TT T
C TC TC TC TC TC T
TAG
CAG
CAG
Phe
Ile
Val
Ser
Tyr
Cys
Phe
Leu
Leu
Leucine
Mutation rate
Synonymous transversion
Synonymous transition
Non-synonymous transversion
Non-synonymous transition
Other
Interpretation
Transition-transversion ratio
dN/dS
Relative viability of non-synonymous mutations
TTTGATACTGTTGCCGAAGGTTTGGGCGAAATTCGCGATTTATTGCGCCGTTATCATCAT
TTTGATACCGTTGCCGAAGGTTTGGGTGAAATTCGCGATTTATTGCGCCGTTACCACCGC
TTTGATACCGTTGCCGAAGGTTTGGGTAAAATTCGCGATTTATTGCGCCGTTACCACCGC
TTTGATACCGTTGCCGAAGGTTTGGGCGAAATTCGTGATTTATTGCGCCGTTATCATCAT
1 2 3 4 5
Evidence for false positives?
Positively selected sites, for which ω > 1
0.0
0.2
0.4
0.6
0.8
1.0
0 50 100 150 200 250
Codon position
Po
ster
ior
pro
bab
ility
Positively selected sites, for which ω > 1
0.0
0.2
0.4
0.6
0.8
1.0
0 50 100 150 200 250
Codon position
Po
ster
ior
pro
bab
ility
www.danielwilson.me.uk
omegaMap