#Minimum Edit Distance
by Yisheng Cai
The minimum cost alignment (Minimum Edit Distance) that finds an O(mn)-time algorithm to find the best alignment of s and t and justify its correctness and running time for given DNA sequences s and t of lengths m and n, respectively, both defined over the alphabet {A,C,G,T}. The algorithm prints out a minimum value of all optimal alignments and
Prepare any input file under the same directory as the program files. The format has to be: -first row is sigma, which is the cost of inserting a gap -in the next four rows, specify a 4x4 matrix with combinations of mismatches of {A, C, G, T} -after inputing the similarity matrix, in next two lines, input two strings consisting of {A, C, G, T}
example: 2 0 1 3 0 1 0 1 2 3 1 0 4 0 2 4 0 AAAGTCTGAC AACGTTTAC
Run program with
$javac *.java
$java Main
$your_input_file_name