3460:435 Algorithms Final Project — DNA Sequence Alignment 05/05/2017
Alyssa Myers & Luciano Mogorovic

General Description
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Comparing two DNA sequences using dynamic programming sequence alignment algorithm.

Execution
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1) Go to the project directory via command line.
2) SeqAlign is to be ran using C++11 compiler.
3) The first command line argument is the first DNA sequence of chars (a/t/c/g).
4) The second command line argument is the second DNA sequence of chars (a/t/c/g).

Sequence Alignment
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o Input of two sequences and create a n * m sized matrix.
  n = length of sequence 1     m = length of sequence 2
o First row = n * gap     First column = m * gap
o For each cell, choose the max, and record in the matrix
  - SCORE { Diagonal Cell + SCORE { i_m, i_n }
          { Left Cell + SCORE { i_m, _ )
          { Top Cell + SCORE { _, j_m }
o Trace back 

Files
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o SeqAlign - main file.
o ScoringMatrix - a 2D vector array that is easily manipulated.
o SeqAligner - functions that perform the sequence alignment algorithm.

Usage
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1) ./SeqAlign sequence1 sequence2