Your program will first prompt the user to enter a single DNA sequence, which it should validate for legality (i. e., only the four valid bases) — you might do this validation by writing a function that takes a String as a parameter and returns a boolean. Re-prompt the user if the input was invalid. Once you have a valid input, compute the following statistics (each should be implemented as a separate function, called from main()).

Count the number of occurrences of "C".

Determine the fraction of cytosine and guanine nucleotides. For example, if half of the nucleotides in the sequence are either "C" or "G", the fraction should be 0.5.

A DNA strand is actually made up of pairs of bases — in effect, two strands that are cross- linked together. These two strands are complementary: if you know one, you can always determine the other, or complement, because each nucleotide only pairs up with one other. In particular, "A" and "T" are complements, as are "C" and "G". So, for example, the com- plement of the sequence "AAGGTCT" would be "TTCCAGA". Compute the complement of the input sequence.

Simple Pairwise Alignments

During reproduction, DNA sequences from both parents are replicated and "mixed" to form the DNA of their offspring. This process is not 100% accurate, and errors, or mutations, creep into the genome. Sometimes, these mutations have no effect, sometimes they are immediately lethal and the offspring isn’t viable, and sometimes they result in changes in characteristics that may make the offspring more competitive when it comes times for it to breed (or may make it more competitive if there is an environmental change). This mutation process is one element that underlies evolution.

A result of evolution is that, after the fact, you can compare two nucleotide sequences and test the hypothesis that they share an evolutionary history. Such comparison allows us to learn how modifications to DNA result in modifications of biochemical processes and physical characteris- tics. This is why sequence alignment techniques are important. We determine an alignment by comparing two sequences and seeing how well they match. A very simple method for this com- parison is to look at corresponding nucleotides and compute a score for that potential alignment. If there ar