Download presentation

Presentation is loading. Please wait.

Published byDevin Prall Modified over 2 years ago

1
Bayesian Evolutionary Distance P. Agarwal and D.J. States. Bayesian evolutionary distance. Journal of Computational Biology 3(1):1— 17, 1996

2
Determining time of divergence Goal: Determine when two aligned sequences X and Y diverged from a common ancestor AGTTGAC ACTTGCC Model: –Mutation only –Independence –Markov process

3
Divergence points have different probabilities Probability X Y Ancestor time

4
DNA PAM matrices Similar to Dayhoff PAM matrices PAM 1 corresponds to 1% mutation –1% change ≈ 10 million years Simplification: uniform mutation rates among nucleotides: –m ij = if i = j –m ij = if i j Can modify to handle different transition/transversion rates –Transitions (A G or C T) have higher probability than transversions PAM x = (PAM 1) x

5
DNA PAM 1 0.99 0.330.99 0.33 0.99 0.33 0.99 A CTG T A G A

6
DNA PAM x (x) (x) (x) (x) (x) (x) (x) A CTG T A G A

7
DNA PAM x As x , (x) and (x) 1/4 Assume p i = ¼ for i ={A,C,T,G} Leads to simple match/mismatch scoring scheme

8
DNA PAM x: Scoring

9
DNA PAM PAM Dist (x) Match score (bits) Mismatch score (bits) 12-6 101.86-3.00 251.66-1.82 501.34-1.04 1000.84-0.44 1250.65-0.3

10
DNA PAM n: Scoring Log-odds score of alignment of length n with k mismatches: Odds score of same alignment: )(4log)( )(4 )( xx xx

11
Probability of k mismatches at distance x Note: Need odds score here, not log-odds!

12
Expected evolutionary distance given k mismatches Over all distances By Bayes’ Thm: Conditional expectation From odds scores ??

13
Assumptions Consider only a finite number of values of x; e.g., 1, 10, 25,50, etc. –In theory, could consider any number of values “Flat prior:” All values of x are equally likely –If M values are considered, Pr(x) = 1/M

14
Calculating Pr(k) and Pr(x|k)

15
Calculating the distance Fraction of the probability of k mismatches that comes from assuming distance is x

16
Ungapped local alignments Only matches and mismatches — no gaps An ungapped local alignment of sequences X and Y is a pair of equal-length substrings of X and Y X Y

17
Ungapped local alignments P. Agarwal and D.J. States. Bayesian evolutionary distance. Journal of Computational Biology 3(1):1—17, 1996 23 matches 2 mismatches 34 matches 11 mismatches A:A: B:B:

18
Which alignment is better? Answer depends on evolutionary distance

Similar presentations

Presentation is loading. Please wait....

OK

DNA sequences alignment measurement

DNA sequences alignment measurement

© 2018 SlidePlayer.com Inc.

All rights reserved.

Ads by Google

Ppt on case study of drought in india Ppt on software quality in software project management Ppt on 26 11 mumbai attacks Ppt on life study of mathematician turing Ppt on water pollution in delhi Ppt on applied operational research journal Ppt on carl friedrich gauss Ppt on product and service design Ppt on 2 dimensional figures and 3 dimensional slides to dvd Ppt on identity property of multiplication