Short Primer on Comparative Genomics

Today: Special guest lecture12pm, Alway M108 Comparative genomics of animals and plants

Adam SiepelAssistant Professor of Biological Statistics and Computational Biology Cornell University

Evolution at the DNA level

…ACGGTGCAGTTACCA…

…AC----CAGTCCACCA…

Mutation

SEQUENCE EDITS

REARRANGEMENTS

Deletion

InversionTranslocationDuplication

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

Orthology, Paralogy, Inparalogs, Outparalogs

Synteny maps

Comparison of human and mouse

Synteny maps

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

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?

Local Alignments

After chaining

Chaining local alignments

1. Find local alignments

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

3. Restricted DP

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

Threaded Blockset Aligner

Human–Cow

HMR – CDRestricted AreaProfile Alignment

Reconstructing the Ancestral Mammalian Genome

Human: C

Baboon: C

Cat: C

Dog: G

C

C or G

G

Neutral Substitution Rates

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

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

Finding Conserved Elements

Finding Conserved Elements (3)

GERP

Phylo HMMs

HMM

Phylogenetic Tree Model

Phylo HMM

Finding Conserved Elements (3)

How do the methods agree/disagree?

Statistical Power to Detect Constraint

L

N

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

Statistical Power to Detect Constraint

L

N

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