CSCI 329 Introduction to Bioinformatics Fall 2013
Global and Local Alignment Dynamic Programming Algorithms Homework

Due Day: Monday, October 21, by e-mail to yanako@cs.widener.edu

You have to send source files and test files.

• Problem 1(50 points): Write a program that finds ALL optimal global alignments and maximal global alignment score between two DNA sequences using dynamic programming Needleman-Wunsch algorithm.
  Your program must print the matrix, the maximal score and all optimal global alignments.
  You have to test your program using visualization website and prepare additional text file that documents your test inputs/outputs
• Problem 2 (50 points): Write a program that finds ALL optimal local alignments and maximal local alignment score between two DNA sequences using dynamic programming Smith-Waterman algorithm. Your program must print the matrix, the maximal score and all optimal local alignments.
  You have to test your program using visualization website and prepare additional text file that documents your test inputs/outputs