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Introduction to Computational and Mathematical Biology

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University of the Philippines Ludwig-Maximilians-University. Diliman Munich, ... Smith-Waterman Algorithm (1) Smith-Waterman Algorithm (2) Local suffix alignment ... – PowerPoint PPT presentation

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Title: Introduction to Computational and Mathematical Biology


1
  • Introduction to Computational and Mathematical
    Biology
  • Lecture 2B
  • Dr. Eduardo Mendoza
  • Mathematics Department Physics
    Department
  • University of the Philippines
    Ludwig-Maximilians-University
  • Diliman Munich, Germany
  • eduardom_at_math.upd.edu.ph
    Eduardo.Mendoza_at_physik.uni-muenchen.de

2
Topics to be covered
  • Local Alignment
  • Motivation
  • Reduction to local suffix alignment
  • End-Space Free Alignment
  • Motivation
  • ESFA-Algorithm

3
Local Alignment Problem
4
Motivation
  • Example 1
  • Example 2

5
An obvious algorithm
but quite slow O(n3m3) Our strategy adapt
global alignment algorithm
6
Definition v(i,j) and example
7
Smith-Waterman Algorithm (1)
8
Smith-Waterman Algorithm (2)
9
Local suffix alignment
10
Local Alignment Algorithm
11
Global vs. local
Diffe
12
Example
13
(No Transcript)
14
Homework (for math majors and others)
  • Prove (or study the proof)
  • What can you say about space requirements
  • O( )? Prove.

15
Homework
  • Find the best local alignment of
  • ATACTACGGAGGG
  • GAACGTAGGCGTAT

16
End-Space Free Alignment
17
Motivation
18
Illustration
19
End-Space Free Alignment Algorithm
20
Recursive definition
21
(No Transcript)
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