Abstract
An essential task in comparative genomics is usually to decompose two or more genomes into synteny blocks, that is, segments of chromosomes with similar contents. In this paper, we study the Maximal Strip Recovery problem (MSR) [Zheng et al. 07], which aims at finding an optimal decomposition of a set of genomes into synteny blocks, amidst possible noise and ambiguities. We present a panel of new or improved FPT and approximation algorithms for the MSR problem and its variants. Our main results include the first FPT algorithm for the variant δ-gap-MSR-d, an FPT algorithm for CMSR-d and δ-gap-CMSR-d running in time O(2.360 k poly(nd)), where k is the number of markers or genes considered as erroneous, and a (d + 1.5)-approximation algorithm for CMSR-d and δ-gap-CMSR-d. © 2011 Springer-Verlag.
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CITATION STYLE
Bulteau, L., Fertin, G., Jiang, M., & Rusu, I. (2011). Tractability and approximability of maximal strip recovery. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6661 LNCS, pp. 336–349). https://doi.org/10.1007/978-3-642-21458-5_29
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