On the consecutive ones property
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
A certifying algorithm for the consecutive-ones property
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Journal of Computer and System Sciences
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
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We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled amniote genomes as ingroups and three teleost fish genomes as outgroups. We combine a methodological framework using conserved syntenies computed from whole genome alignments of amniote species together with double conserved syntenies (DCS) using gene families from amniote and fish genomes, to take into account the whole genome duplication that occurred in the teleost lineage. From these comparisons, ancestral genome segments are computed using techniques inspired by physical mapping. Due to the difficulty caused by the whole genome duplication and the large evolutionary distance to the closest assembled outgroup, very few methods have been published with a reconstruction of the amniote ancestral genome. This one is the first which is founded on a simple and formal methodological framework, whose good stability is shown and whose CARs cover large regions of the human and chicken genomes.