Day 2 Question 3

Aligning DNA

Input file:

Output file: probf.out

You are a biologist studying various patterns in DNA sequences. You need a program that will find regions of similarity in a pair of sequences, and align the similar regions by inserting spaces into the sequences.

A DNA sequence is represented as a string of characters from the set {A, C, G, T}.

For example, if you were given the sequences:


your program would insert two spaces before the second sequence to align the TCGA. The aligned sequences would be:


where the dashes represent spaces. In every alignment, the lengths of the two sequences (including spaces) must be equal, although the original sequences need not be of the same length.

We will assign a number of points to each alignment, and we will call the alignment with the highest number of points the best alignment. To calculate the number of points, we proceed character by character from the beginning of the sequence. For each position, we get a certain number of points:

For example, with the alignment:


we would lose one point for the first position (A,-), another point for the second position (C,G) and gain three points for the last position (T,T), for a total of one point.

Your program will be given pairs of DNA sequences. It must find the best alignment, along with the number of points given to that alignment. If there is more than one alignment with the highest number of points, any one of the best alignments is acceptable.

The input will consist of pairs of lines, each line no longer than 100 characters. Each line represents a DNA sequence, and you are to align the two sequences in each pair of lines (ie, align each odd-numbered line with the line that comes after it). The last line of the input will consist of a single asterisk. The input will not contain any lower-case letters.

The output is to consist of three lines for each pair of sequences. The first line will be a single integer representing the number of points assigned to that alignment. The next two lines will consist of the aligned sequences, in the same order as they were read in, with spaces represented by dashes (-). The output shall not contain any lower-case letters.