Project :Sequence Alignment and Substitution Matrices

Project :Sequence Alignment and Substitution Matrices Input Specs: Allow the user to select peptide (protein, amino acid sequence) or nucleotide sequence files in FASTA format, prompting for the FASTA format filename and sequence type (peptide versus nucleotide). Allow the user to select a matrix of amino acid substitution scores (e.g. BLOSUM, PAM(n), hydrophobicity) in the formats provided in zipped folder P1SubMatrices. You should also allow as input your PAM(n) matrix files, despite the different delimiter format. Notice the amino acid order in all matrices: A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V For input nucleotide sequences, you may find the matrix [login to view URL] helpful, as it simulates the following nucleotide substitution matrix: A C T G A 4 -2 -2 1 C -2 4 1 -2 T -2 1 4 -2 G 1 -2 -2 4 Algorithmic Specs: Allow the user to select what kind of alignment is desired: global, local, or semiglobal. Have the user input gap penalties. You will use the substitution matrix to perform a protein alignment of the two amino acid sequences. Additionally, allow user to select affine alignment as one of the alignment types. If affine is selected, then the user should separately input the gap start penalty and the gap extension penalty. For any alignment type chosen, your algorithm must take Q(n2) time . Output Specs: Output both your OPT matrix (in the case of affine that includes 3 matrices) and your optimal alignment in a readable form to the console. In the case of ties, you need output only one optimal alignment (not all ties). What to turn in: You must turn in a single zipped file containing your source code, a Makefile if needed for compilation, and a README file indicating how to compile/execute your program Program must be written in C/C++,