Computing the Family-Free DCJ Similarity
Speaker: Jens Stoye, Bielefeld University.
Date: 14 mar 2018, 13h.
Place: Room 407, Bloco H, Campus Gragoatá, UFF.
Abstract: The genomic similarity is a large-scale measure for comparing two given genomes. In this talk we present the (NP-hard) problem of computing the genomic similarity under the DCJ model in a setting that does not assume that the genes of the compared genomes are grouped into gene families. This problem is called family-free DCJ similarity. We propose an exact ILP algorithm to solve the family-free DCJ similarity problem, then we show its APX-hardness and present four combinatorial heuristics with computational experiments comparing their results to the ILP. We show that the family-free DCJ similarity can be computed in reasonable time, although for larger genomes it is necessary to resort to heuristics. This provides a basis for further studies on the applicability and model refinement of family-free whole genome similarity measures.
Joint work with Diego P. Rubert, Edna A. Hoshino, Marília D. V. Braga and Fábio V. Martinez.