NDLI: Genetic Design of Drugs Without Side-Effects

Content Provider	Society for Industrial and Applied Mathematics (SIAM)
Author	Li, Guojun Li, Zimao Deng, Xiaotie Ma, Bin Wang, Lusheng
Copyright Year	2003
Abstract	Consider two sets of strings, ${\cal B}$ (bad genes) and ${\cal G}$ (good genes), as well as two integers $d_b$ and $d_g$ ($d_b\leq d_g$). A frequently occurring problem in computational biology (and other fields) is to find a (distinguishing) substring s of length L that distinguishes the bad strings from good strings, i.e., such that for each string $s_i\in {\cal B}$ there exists a length-L substring ti of si with $d(s, t_i)\leq d_b$ (close to bad strings), and for every substring ui of length L of every string $g_i\in {\cal G}$, $d(s, u_i)\geq d_g$ (far from good strings).We present a polynomial time approximation scheme to settle the problem; i.e., for any constant $\epsilon >0$, the algorithm finds a string s of length L such that for every $s_i\in {\cal B}$ there is a length-L substring ti of si with $d(t_i, s)\leq (1+\epsilon) d_b$, and for every substring ui of length L of every $g_i\in {\cal G}$, $d(u_i, s)\geq (1-\epsilon) d_g$ if a solution to the original pair ($d_b\leq d_g$) exists. Since there is a polynomial number of such pairs $(d_b,d_g)$, we can exhaust all the possibilities in polynomial time to find a good approximation required by the corresponding application problems.
Starting Page	1073
Ending Page	1090
Page Count	18
File Format	PDF
ISSN	00975397
DOI	10.1137/S0097539701397825
e-ISSN	10957111
Journal	SIAM Journal on Computing (SMJCAT)
Issue Number	4
Volume Number	32
Language	English
Publisher	Society for Industrial and Applied Mathematics
Publisher Date	2003-01-01
Access Restriction	Subscribed
Subject Keyword	computational molecular biology Protein sequences, DNA sequences Approximation algorithms approximation algorithms Combinatorial optimization distinguishing substring selection
Content Type	Text
Resource Type	Article
Subject	Mathematics Computer Science

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