Find All Approximate Occurrences of a Pattern in a String solved by 445

July 29, 2015, 1:08 a.m. by Rosalind Team

We say that a k-mer Pattern appears as a substring of Text with at most d mismatches if there is some k-mer substring Pattern' of Text having d or fewer mismatches with Pattern, i.e., HammingDistance(Pattern, Pattern') ≤ d. Our observation that a DnaA box may appear with slight variations leads to the following generalization of the Pattern Matching Problem.

Approximate Pattern Matching Problem

Find all approximate occurrences of a pattern in a string.

Given: Strings Pattern and Text along with an integer d.

Return: All starting positions where Pattern appears as a substring of Text with at most d mismatches.

Sample Dataset

ATTCTGGA
CGCCCGAATCCAGAACGCATTCCCATATTTCGGGACCACTGGCCTCCACGGTACGGACGTCAATCAAATGCCTAGCGGCTTGTGGTTTCTCCTACGCTCC
3

Sample Output

6 7 26 27 78

Extra Datasets

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