d-Neighborhood of a String (d-Neighborhood of a String)
Revision as of 10:25, 15 February 2023 by Admin (talk | contribs) (Created page with "{{DISPLAYTITLE:d-Neighborhood of a String (d-Neighborhood of a String)}} == 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 == <pre>n: length of string d: neighborhood distance threshold sigma: size of alphabet</pre> == Table of Algorithms == {| cla...")
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 |