Multiple sequence alignment Chapter 5 Xiong Book Definition

Multiple sequence alignment Chapter 5, Xiong Book

Definition

Multiple sequence alignment are often done by heuristic approaches.

Sum-of-Pairs

Heuristic multiple sequence alignment algorithms

Clustal -A progressive multiple alignment program

Progressive alignment method

Progressive alignment method, cont’d

Progressive alignment method, cont’d

Guide tree This is a “greedy” method.

What is a greedy method? • A greedy method breaks a large problem into small ones (stages) and chooses the best approach at each stage. • Examples: – Making changes using quarters, dimes, nickels, and pennies. (Greedy solution is the optimal solution). – Rock climbing. (Greedy solution may not be the optimal solution but is still practically useful one. ) • It may or may not be the perfect solution depending on the problem and how it is partitioned.

Clustal

Drawbacks of progressive programming

T-coffee (not required for exam)

T-coffee

T-coffee

Heuristic multiple sequence alignment algorithms

Iterative alignment (not required)

Heuristic multiple sequence alignment algorithms

Block-based alignment (not required)

DIALIGN

Practical issues of sequence alignment

Alignment of protein-coding DNA sequences (Required)

Alignment Editing

Bio. Edit

Readseq

Summary • Clustal – Guide tree – Greedy nature – Global alignment • How to align protein-coding DNA sequences?

Reading Assignment Chapter 5, Xiong Book