The approximability of the String Barcoding problem

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. Background The following setting was introduced by Rash and Gusfield in [1]: Given a set V of n strings v1,...,vn (representing the genomes of n known viruses), and an extra string s (representing a virus in V, but not yet classified), we aim at recognizing ...

• Type: Journal
• Year: 2006
• Where: ALMOB
• Authors: Giuseppe Lancia, Romeo Rizzi
• Keywords: ALMOB 2006, Computational Biology Context, Rash, Viruses