Tractability and approximability of maximal strip recovery

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 ', by deleting the minimum number k = n' of markers which are likely 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 2O(d ')poly(nd) time FPT algorithm for -gap-MSR-d, a 2:36kpoly(nd) time FPT algorithm for both CMSR-d and -gap-CMSR-d, and a (d+1:5)-approximation algorithm for both CMSR-d and -gap-CMSR-d.
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Submitted on : Wednesday, May 23, 2012 - 3:02:34 PM
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Laurent Bulteau, Guillaume Fertin, Minghui Jiang, Irena Rusu. Tractability and approximability of maximal strip recovery. Theoretical Computer Science, Elsevier, 2012, 440-441, pp.14-28. ⟨10.1016/j.tcs.2012.04.034⟩. ⟨hal-00700598⟩



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