Programming assignments #2 and #3 Kun-Mao Chao March 17, 2003.

Due: March 31 and April 7, 2003.

Sequence alignment with a simple scoring scheme

Input Format

Match (a bonus score for a match)

Mismatch (a penalty for a mismatch)

Gapsymbol (a penalty for a gap symbol)

First sequence starting with a line “>Sequence 1”

Second sequence starting with a line “>Sequence 2”

The input file is terminated by a line with the number 0.

Output

1. Report the score of an optimal global alignment (Due: 3/31/2003)

2. Report an optimal global alignment (Due: 3/31/2003)

3. Report the score of an optimal local alignment (Due: 4/7/2003)

4. Report an optimal local alignment (Due: 4/7/2003)

Sample Input

8

-5

-3

>Sequence 1

GCGCATGGATT

>Sequence 2

TGCGCCATGGAT

0

Sample Output

The score of an optimal global alignment is 71.

An optimal global alignment:

-GCG-CATGGATT

TGCGCCATGGAT-

The score of an optimal local alignment is 77.

An optimal local alignment:

GCG-CATGGAT

GCGCCATGGAT