Find All Shared k-mers of a Pair of Strings solved by 172

Jan. 21, 2014, 12:06 a.m. by Rosalind Team

Figure 1. The shared 3-mers of AAACTCATC and TTTCAAATC. The second pair are shown in blue because they are reverse complementary. The four pairs of shared *k*-mers can be represented by the ordered pairs (0,4), (0,0), (4,2), and (6,6).

We say that a k-mer is shared by two genomes if either the k-mer or its reverse complement appears in each genome. In Figure 1 are four pairs of 3-mers that are shared by "AAACTCATC" and "TTTCAAATC".

A shared k-mer can be represented by an ordered pair (x, y), where x is the starting position of the k-mer in the first genome and y is the starting position of the k-mer in the second genome. For the genomes "AAACTCATC" and "TTTCAAATC", these shared k-mers are (0,4), (0,0), (4,2), and (6,6).

Shared k-mers Problem

Given two strings, find all their shared k-mers.

Given: An integer k and two strings.

Return: All k-mers shared by these strings, in the form of ordered pairs (x, y) corresponding to starting positions of these k-mers in the respective strings.

Sample Dataset

3
AAACTCATC
TTTCAAATC

Sample Output

(0, 4)
(0, 0)
(4, 2)
(6, 6)

Extra Dataset

Please login to solve this problem.