Swiftly Computing Center Strings
The center string (or closest string) problem is a classical computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance d to each input string. This problem is NP-complete. In this paper, we focus on exact methods for the problem that are also fast in application. First, we introduce data reduction techniques that allow us to infer that certain instances have no solution, or that a center string must satisfy certain conditions. Then, we describe a novel search tree strategy that is very efficient in practice. Finally, we present results of an evaluation study for instances from a biological application. We find that data reduction is mandatory for the notoriously difficult case d = d opt− 1.
KeywordsSearch Tree Close String Binary String Distance Threshold Input String
Unable to display preview. Download preview PDF.
- 8.Rahmann, S., Klau, G.W.: Integer linear programming techniques for discovering approximate gene clusters. In: Mandoiu, I., Zelikovsky, A. (eds.) Bioinformatics Algorithms: Techniques and Applications. Wiley Series on Bioinformatics: Computational Techniques and Engineering, ch. 9, pp. 203–222. Wiley, Chichester (2008)Google Scholar
- 10.Wang, Y., Chen, W., Li, X., Cheng, B.: Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cdna. BMC Bioinformatics 7(suppl. 4), S9 (2006)Google Scholar
- 11.Yanai, I., DeLisi, C.: The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 3(11), research0064 (2002)Google Scholar