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DIVERSIFYING SELECTION AND FUNCTIONAL CONSTRAINT. ESTIMATING THE dN/dS RATIO FOR GENE SEQUENCES IN THE PRESENCE OF RECOMBINATION. Danny Wilson 18 th August 2005. Example: CTT. C. T. T. T. T. T. A. T. T. Leucine. G. T. T. C. C. T. C. A. T. C. G. T. C. T. C. C. T. A. - PowerPoint PPT Presentation
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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
