Download Finding Approximate Multiple Alignment

Finding Approximate Multiple
Alignment
Bo Brinkman and Martin Tompa
Abstract
We develop an algorithm which finds approximately optimal
alignments for the general case of k sequences. Our goal is to
increase the effectiveness of known methods (such as dynamic
programming) by applying them in a new way.
1. Introduction
2. The Basic Algorithm
1. Split the k sequences into two groups using some method
2. Align these two groups to each other using dynamic programming
3. Treat the output alignment as a list of sequences, and go to step 1
3. Scoring function
3.1 Relative Entropy Scoring of DNA
DP ab
 g ab Bk

g Bk 
t
|| B   
lg
 Bk
t


ab






3.2 SP-Measure Dayhoff Scoring for Proteins
In our program we use the SP-measure along with a scoring
matrix which assigns a score to the pairing of any two amino
acids.
4. Grouping Techniques
5. Concluding Remarks
1. Tuning Gap and Space Penalties
2. Explore Effect of Local Optima
3. More Advanced Grouping Methods
Created by : Kuen-Feng Huang
Date : May. 31, 2000