d-Neighborhood of a String (d-Neighborhood of a String)
Jump to navigation
Jump to search
Description
Given a DNA string pattern and an integer $d$, find the collection of strings that are within a $d$-neighborhood of the given pattern. A $d$-neighborhood is the set of all $k$-mers whose Hamming distance from the pattern is at most $d$.
Parameters
n: length of string
d: neighborhood distance threshold
sigma: size of alphabet
Table of Algorithms
| Name | Year | Time | Space | Approximation Factor | Model | Reference |
|---|---|---|---|---|---|---|
| Iterative naive | 1940 | $O(f_{bin}(sigma-{1}, n, d)$) where f_{bin}(x, y, z) = sum_{i=0}^z C(y, i)*x^i | $O(n)$ auxiliary | Exact | Deterministic | Time |