Finding All Similar Motifs solved by 60

May 11, 2013, 10:48 a.m. by mariel.21

Topics: String Algorithms

The Case of Mutated Repeats

In “Finding a Motif with Modifications”, we considered a problem in which we were given a motif and a long string (perhaps representing a genome), and we aimed to find the "closest" substring of the long string to the motif. In that problem, "closest" was defined as a minimum with respect to edit distance.

Yet there may be multiple substring candidates from the genome that achieve the minimum distance to the motif; this situation might occur in practice when the motif forms a repeat that occurs multiple times with variations deriving from mutations.

In this problem, we would like to find all substrings of a genome that are within a certain fixed distance of the desired motif.

Problem

Given: A positive integer $k$ ($k \leq 50$), a DNA string $s$ of length at most 5 kbp representing a motif, and a DNA string $t$ of length at most 50 kbp representing a genome.

Return: All substrings $t'$ of $t$ such that the edit distance $d_{\mathrm{E}}(s, t')$ is less than or equal to $k$. Each substring should be encoded by a pair containing its location in $t$ followed by its length.

Sample Dataset

2
ACGTAG
ACGGATCGGCATCGT

Sample Output

1 4
1 5
1 6

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