The approximability of the String Barcoding problem

The approximability of the String Barcoding problem

<p>Abstract</p> <p>The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given string...

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Main Authors: Rizzi Romeo, Lancia Giuseppe
Format: Article
Language:English
Published: BMC 2006-08-01
Series:Algorithms for Molecular Biology
Online Access:http://www.almob.org/content/1/1/12
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spelling doaj-2fa7f66297bb47afb2c291c31719d6012020-11-25T00:28:04ZengBMCAlgorithms for Molecular Biology1748-71882006-08-01111210.1186/1748-7188-1-12The approximability of the String Barcoding problemRizzi RomeoLancia Giuseppe<p>Abstract</p> <p>The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight.</p> http://www.almob.org/content/1/1/12
collection DOAJ
language English
format Article
sources DOAJ
author Rizzi Romeo
Lancia Giuseppe
spellingShingle Rizzi Romeo
Lancia Giuseppe
The approximability of the String Barcoding problem
Algorithms for Molecular Biology
author_facet Rizzi Romeo
Lancia Giuseppe
author_sort Rizzi Romeo
title The approximability of the String Barcoding problem
title_short The approximability of the String Barcoding problem
title_full The approximability of the String Barcoding problem
title_fullStr The approximability of the String Barcoding problem
title_full_unstemmed The approximability of the String Barcoding problem
title_sort approximability of the string barcoding problem
publisher BMC
series Algorithms for Molecular Biology
issn 1748-7188
publishDate 2006-08-01
description <p>Abstract</p> <p>The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight.</p>
url http://www.almob.org/content/1/1/12
work_keys_str_mv AT rizziromeo theapproximabilityofthestringbarcodingproblem
AT lanciagiuseppe theapproximabilityofthestringbarcodingproblem
AT rizziromeo approximabilityofthestringbarcodingproblem
AT lanciagiuseppe approximabilityofthestringbarcodingproblem
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