ADDIS ABABA SCIENCE AND TECHNOLOGY

UNIVERSTY

College of Biological and Chemical Engineering

Department of Biotechnology

Bioinformatics

Assignment
Global and local alignment

Name ID
NETSANET MOLLA GSR310/14

Submitted to Dr. Adugna Abdi

1|Page by Netsanet Molla

Problem 1.
1. What is the optimal global alignment for APPLE and HAPPE?
2. Show all optimal alignments and the corresponding paths under the matching premium +1,
mismatch penalty −1, and indel penalty −1.

The high score of the global alignment is 2

The optimal alignment is:

-1 1 1 1 -1 1

The sum is 2

2|Page by Netsanet Molla

3. Do the same procedure as above for both APPLE and HAPPE to arrive at the optimal local
alignment using the same parameters given for match/mismatch and penalty.

The high score of optimal alignment is: 3

The local optimal sequence alignment is

Problem2

3|Page by Netsanet Molla

1. Consider the sequences v = TACGGGTAT and w = GGACGTACG. Assume that the matching
premium is +1 and that the mismatch and gap penalties are −1. Fill out the dynamic
programming table for a global alignment between v and w.
2. Draw arrows in the cells to store the backtrack information. What is the score of the optimal
global alignment and what alignment does this score correspond to?
Answer
v = TACGGGTAT

w = GGACGTACG eve

The score of the optimal global alignment is 1

All possible global alignments are:
Global alignment 1

-1 -1 1 1 1 -1 -1 1 1
The sum is +1
Global alignment 2

4|Page by Netsanet Molla

-1 -1 1 1 1 -1 -1 1 1
The sum is +1
Global alignment3

-1 -1 1 1 -1 -1 1 1 1
The sum is +1
Global alignment4

-1 -1 1 1 -1 -1 1 1 1
The sum is +1

5|Page by Netsanet Molla

3. Fill out the dynamic programming table for a local alignment between v and w. Draw arrows
in the cells to store the backtrack information. What is the score of the optimal local alignment
in this case and what alignment achieves this score?
Match premium 1, Gap penalty -1, mismatch -1

High score of optimal local alignment is 4

Optimal local sequence alignment is

1 1 1 1
The sum is 4

6|Page by Netsanet Molla