I developed an algorithm for solving protein sequence alignment
which aims to find optimum matching between two amino acid sequences.
Inputs are: two given strings x, y where length(x)=m and length(y)=n, and a cost matrix C which prescribes a
cost for matching and mismatching characters. A gap penalty is the component deducted from
alignment score due to the presence of a gap, i.e., matching of a letter in one sequence with a
dash (space) in the other sequence. A gap penalty may be a function of the length of the gap;
for example, a linear gap penalty is a constant g such that each inserted or deleted symbol is
charged g; the total cost of a gap of length L is equal to gL.
1.Two protein strings x and y, each one is in one line of the file (at most 1000 amino acid)
2.Cost matrix (BLOSUM62 scoring matrix)
3.Linear gap penalty equal to -5 (i.e., a cost of -5 is assessed for each gap symbol)
1.The maximum alignment score between x and y.
2.Best alignment between x and y.