CS 4329 Introduction to bioinformatics.

All code must be written in C++ (C++ was also used in CS1, CS2, and CS3). You should submit

The source codes.

A document showing the output for test cases.

Put all the individual files in one single folder and compress the folder. Upload the compressed folder. Files

should include your first and last names.

1. Implement a C++ function to compute the score of a multiple sequence alignment using Entropy method

(incorporate gaps) and also output the profile of the alignment. Note that your function should be able

detect the number of sequences and the alignment length in the multiple alignment. The alignment

should be read from a text file. Note that pX log2pX is 0 if pX is 0. [100 points]

Test Case 1:

AAA

ACC

ACG

ACT

Output should be

Alignment profile:

A 4 1 1

T 0 0 1

G 0 0 1

C 0 3 1

- 0 0 0

Entropy score is 2.811

Test Case 2:

AAACC

ACG

ACOutput

should be

Alignment profile:

A 4 1 0

T 0 0 0

G 0 0 1

C 0 3 1

- 0 0 2

Entropy score is 2.311

Test Case 3:

GGGCGGTAA

GGGAA

Output should be

Alignment profile:

A 0 0 0 2 2

T 0 0 1 0 0

G 3 3 2 0 0

C 0 0 0 1 0

- 0 0 0 0 1

Entropy score is 2.755