Bioinformatický seminár

Tue 27 Sep. 2011, 17:20

Title: Chauve et al. Yeast ancestral genome reconstructions: the possibilities of computational methods II
Speaker: Kubo Kováč

Since the availability of assembled eukaryotic genomes, the first one
being a budding yeast, many computational methods for the reconstruction
of ancestral karyotypes and gene orders have been developed. The
difficulty has always been to assess their reliability, since we often
miss a good knowledge of the true ancestral genomes to compare their
results to, as well as a good knowledge of the evolutionary mechanisms to
test them on realistic simulated data. In this study, we propose some
measures of reliability of several kinds of methods, and apply them to
infer and analyse the architectures of two ancestral yeast genomes, based
on the sequence of seven assembled extant ones. The pre-duplication common
ancestor of S. cerevisiae and C. glabrata has been inferred manually by
Gordon et al. (Plos Genet. 2009). We show why, in this case, a good
convergence of the methods is explained by some properties of the data,
and why results are reliable. In another study, Jean et al. (J. Comput
Biol. 2009) proposed an ancestral architecture of the last common ancestor
of S. kluyveri, K. thermotolerans, K. lactis, A. gossypii, and Z. rouxii
inferred by a computational method. In this case, we show that the dataset
does not seem to contain enough information to infer a reliable
architecture, and we construct a higher resolution dataset which gives a
good reliability on a new ancestral configuration.