Motif Search

Description

Motif search is the problem of identifying motifs, recurring or conserved patterns, in the strings (typically biological sequence data sets).

Parameters

$n$: size of set of input strings

$m$: size of input strings

$k$: length of substrings

$\sigma$: function $V(k, m)$ defined as the number of $k$-mers that are at most $m$ Hamming distance from the motif space

Table of Algorithms

Name	Year	Time	Space	Approximation Factor	Model	Reference
Lawrence, Reilly	1990	$O(nm)$	$O(nm)$		Deterministic	Time & Space
Lawrence Gibbs Sampling	1993	$O(nm)$	$O(n + m)$		Deterministic	Time
MotifSampler	2001	$O(nm)$	$O(n + m)$		Deterministic	Time
Speller	1998	$O(mn^{2} \sigma)$	$O(mn^{2}/w)$	Exact	Deterministic	Time & Space
Mitra	2002	$O(k nm \sigma)$	$O(mnk)$	Exact	Deterministic	Time & Space
Census	2003	$O(k nm \sigma)$	$O(mnk)$	Exact	Deterministic	Time & Space
Risotto	2006	$O(mn^{2} \sigma)$	$O(mn^{2})$	Exact	Deterministic	Time & Space
PMS	2007	$O(nm^{2} \sigma)$	$O(m^{2} n)$	Exact	Deterministic	Time & Space
Roth AlignACE	1998	$O(nm)$	$O(n + m)$		Deterministic	Time
Helden Oligo-Analysis	1998	$O(nm)$	$O(m)$	Exact	Deterministic	Time
van Helden J; Rios AF; Collado-Vides J	2000	$O(nm)$	$O(m)$	Exact	Deterministic	Time
Tompa M	1999	$O(nm)$	$O(m^{2})$	Exact	Deterministic	Time
Sinha S; Tompa M YMF (Yeast Motif Finder)	2000	$O(n^{0.{6}6} m)$	$O(m)$	Exact	Deterministic	Time
Bailey TL; Elkan C MEME	1995	$O(n^{2}m^{2})$	$O(nm)$	Exact	Deterministic	Time
Sagot M	1988	$O(n log(n) m^{1.45})$	$O(mn^{2}/w)$	Exact	Deterministic	Time & Space
Liang Cwinnower	2003	$O(nm^{0.5})$	$O(m^{2})$	Exact	Deterministic	Time
Kingsford	2006	$O(mn)$	$O(m^{2}n^{2})$	Exact	Deterministic	Time

Time Complexity Graph

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Space Complexity Graph

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Time-Space Tradeoff

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