Fingerprint Clustering with Bounded Number of Missing Values
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The problem of clustering fingerprint vectors with missing values is an interesting problem in Computational Biology that has been proposed in Figueroa et al. (J. Comput. Biol. 11(5):887–901, 2004). In this paper we show some improvements in closing the gaps between the known lower bounds and upper bounds on the approximability of variants of the biological problem. Moreover, we have studied two additional variants of the original problem proposed in Figueroa et al. (Proc. 11th Computing: The Australasian Theory Symposium (CATS), CRPIT, vol. 41, pp. 57–60, 2005). We prove that all such problems are APX-hard even when each fingerprint contains only two unknown positions and we present a greedy algorithm that has constant approximation factors for these variants. Despite the hardness of these restricted versions of the problem, we show that the general clustering problem on an unbounded number of missing values such that they occur for every fixed position of an input vector in at most one fingerprint is polynomial time solvable.
KeywordsClustering Approximation algorithm Fingerprint vectors
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- 5.Drmanac, S., Drmanac, R.: Processing of cDNA and genomic kilobase-size clones for massive screening mapping and sequencing by hybridization. Biotechniques 17, 328–336 (1994) Google Scholar
- 8.Figueroa, A., Goldstein, A., Jiang, T., Kurowski, M., Lingas, A., Persson, M.: Approximate clustering of fingerprint vectors with missing values. In: Proc. 11th Computing: The Australasian Theory Symposium (CATS). CRPIT, vol. 41, pp. 57–60 (2005) Google Scholar
- 9.Papadimitriou, C.H.: Computational Complexity. Addison–Wesley, Reading (1993) Google Scholar
- 11.Valinsky, L., Della Vedova, G., Scupham, A., Alvey, S., Figueroa, A., Yin, B., Hartin, R., Chrobak, M., Crowley, D., Jiang, T., Borneman, J.: Analysis of bacterial microbial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68(7), 3243–3250 (2002) CrossRefGoogle Scholar