Implement MotifEnumeration solved by 286

July 29, 2015, 12:29 a.m. by Rosalind Team

Given a collection of strings Dna and an integer d, a k-mer is a (k,d)-motif if it appears in every string from Dna with at most d mismatches. The following algorithm finds (k,d)-motifs.

    MOTIFENUMERATION(Dna, k, d)
        Patterns ← an empty set
        for each k-mer Pattern in Dna
            for each k-mer Pattern’ differing from Pattern by at most d
             mismatches
                if Pattern' appears in each string from Dna with at most d
               mismatches
                    add Pattern' to Patterns
        remove duplicates from Patterns
        return Patterns

Implanted Motif Problem

Implement MotifEnumeration (shown above) to find all (k, d)-motifs in a collection of strings.

Given: Integers k and d, followed by a collection of strings Dna.

Return: All (k, d)-motifs in Dna.

Sample Dataset

3 1
ATTTGGC
TGCCTTA
CGGTATC
GAAAATT

Sample Output

ATA ATT GTT TTT

Extra Datasets

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