Tractability and approximability of maximal strip recovery

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Abstract

An essential task in comparative genomics is to decompose two or more genomes into synteny blocks that are segments of chromosomes with similar contents. Given a set of d genomic maps each containing the same n markers without duplicates, the problem Maximal Strip Recovery (MSR) aims at finding a decomposition of the genomic maps into synteny blocks (strips) of the maximum total length ℓ, by deleting the minimum number k=n-ℓ of markers which are probably noise and ambiguities. In this paper, we present a collection of new or improved FPT and approximation algorithms for MSR and its variants. Our main results include a 2 O(dδℓ)poly(nd) time FPT algorithm for δ-gap-MSR-d, a 2.36 kpoly(nd) time FPT algorithm for both CMSR-d and δ-gap-CMSR-d, and a (d+1.5)-approximation algorithm for both CMSR-d and δ-gap-CMSR-d. © 2012 Elsevier B.V. All rights reserved.

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Bulteau, L., Fertin, G., Jiang, M., & Rusu, I. (2012). Tractability and approximability of maximal strip recovery. Theoretical Computer Science, 440441, 14–28. https://doi.org/10.1016/j.tcs.2012.04.034

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