Homework assignments #2         Kun-Mao Chao 

Handout: Oct. 22, 2008.

Due: Nov. 17, 2008

 

Sequence alignment in linear space 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

2.          Report an optimal global alignment

3.          Report the score of an optimal local alignment

4.          Report an optimal local alignment

 

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

　

　

More sequences: rabbit_short  human_short  rabbit_medium  human_medium  rabbit_long  human_long