CS273a Lecture 9/10, Aut 10, Batzoglou

Multiple Sequence Alignment

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Evolution at the DNA level

…ACGGTGCAGTTACCA…

…AC----CAGTCCACCA…

Mutation

SEQUENCE EDITS

REARRANGEMENTS

Deletion

InversionTranslocationDuplication

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Orthology and Paralogy

HB HumanHB Human

WB WormWB Worm

HA1 HumanHA1 Human

HA2 HumanHA2 Human

YeastYeast

WA WormWA Worm

Orthologs:Derived by speciation

Paralogs:Everything else

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Orthology, Paralogy, Inparalogs, Outparalogs

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Genome Evolution – Macro Events

• Inversions• Deletions• Duplications

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Synteny maps

Comparison of human and mouse

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Synteny maps

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Synteny maps

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Synteny maps

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Building synteny maps

Recommended local aligners• BLASTZ

Most accurate, especially for genes Chains local alignments

• WU-BLAST Good tradeoff of efficiency/sensitivity Best command-line options

• BLAT Fast, less sensitive Good for

• comparing very similar sequences • finding rough homology map

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Index-based local alignment

Dictionary:

All words of length k (~10)

Alignment initiated between words of alignment score T

(typically T = k)

Alignment:

Ungapped extensions until score

below statistical threshold

Output:

All local alignments with score

> statistical threshold

……

……

query

DB

query

scan

Question: Using an idea from overlap detection, better way to find all local alignments between two genomes?

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Local Alignments

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

After chaining

CS273a Lecture 9/10, Aut 10, Batzoglou

Chaining local alignments

1. Find local alignments

2. Chain -O(NlogN) L.I.S.

3. Restricted DP

CS273a Lecture 9/10, Aut 10, Batzoglou

Progressive Alignment

• When evolutionary tree is known:

Align closest first, in the order of the tree In each step, align two sequences x, y, or profiles px, py, to generate a new

alignment with associated profile presult

Weighted version: Tree edges have weights, proportional to the divergence in that edge New profile is a weighted average of two old profiles

x

w

y

z

Example

Profile: (A, C, G, T, -)px = (0.8, 0.2, 0, 0, 0)py = (0.6, 0, 0, 0, 0.4)

s(px, py) = 0.8*0.6*s(A, A) + 0.2*0.6*s(C, A) + 0.8*0.4*s(A, -) + 0.2*0.4*s(C, -)

Result: pxy = (0.7, 0.1, 0, 0, 0.2)

s(px, -) = 0.8*1.0*s(A, -) + 0.2*1.0*s(C, -)

Result: px- = (0.4, 0.1, 0, 0, 0.5)

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Threaded Blockset Aligner

Human–Cow

HMR – CDRestricted AreaProfile Alignment

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Reconstructing the Ancestral Mammalian Genome

Human: C

Baboon: C

Cat: C

Dog: G

C

C or G

G

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Neutral Substitution Rates

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Finding Conserved Elements (1)

• Binomial method 25-bp window in the human genome Binomial distribution of k matches in N bases given the neutral

probability of substitution

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Finding Conserved Elements (2)

• Parsimony Method Count minimum # of mutations explaining each column Assign a probability to this parsimony score given neutral model Multiply probabilities across 25-bp window of human genome

A

CAAG

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Finding Conserved Elements

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Finding Conserved Elements (3)

GERP

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Phylo HMMs

HMM

Phylogenetic Tree Model

Phylo HMM

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Finding Conserved Elements (3)

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

How do the methods agree/disagree?

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Statistical Power to Detect Constraint

L

N

C: cutoff # mutationsD: neutral mutation rate: constraint mutation rate relative to neutral

CS273a Lecture 9/10, Aut 10, BatzoglouCS273a Lecture 10, Fall 2010

Statistical Power to Detect Constraint

L

N

C: cutoff # mutationsD: neutral mutation rate: constraint mutation rate relative to neutral