Finding a Spliced Motif solved by 2710

July 13, 2012, midnight by Rosalind Team

Topics: String Algorithms

Motifs Are Rarely Contiguous

In “Finding a Motif in DNA”, we searched for occurrences of a motif as a substring of a larger database genetic string. However, because a DNA strand coding for a protein is often interspersed with introns (see “RNA Splicing”), we need a way to recognize a motif that has been chopped up into pieces along a chromosome.

Problem

A subsequence of a string is a collection of symbols contained in order (though not necessarily contiguously) in the string (e.g., ACG is a subsequence of TATGCTAAGATC). The indices of a subsequence are the positions in the string at which the symbols of the subsequence appear; thus, the indices of ACG in TATGCTAAGATC can be represented by (2, 5, 9).

As a substring can have multiple locations, a subsequence can have multiple collections of indices, and the same index can be reused in more than one appearance of the subsequence; for example, ACG is a subsequence of AACCGGTT in 8 different ways.

Given: Two DNA strings $s$ and $t$ (each of length at most 1 kbp) in FASTA format.

Return: One collection of indices of $s$ in which the symbols of $t$ appear as a subsequence of $s$. If multiple solutions exist, you may return any one.

Sample Dataset

>Rosalind_14
ACGTACGTGACG
>Rosalind_18
GTA

Sample Output

3 8 10

Extra Information

For the mathematically inclined, we may equivalently say that $t = t_1 t_2 \cdots t_m$ is a subsequence of $s = s_1 s_2 \cdots s_n$ if the characters of $t$ appear in the same order within $s$. Even more formally, a subsequence of $s$ is a string $s_{i_1} s_{i_2} \ldots s_{i_k}$, where $1 \leq i_1 < i_2 \cdots < i_k \leq n$.

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