Data: 29/03/2017

Palestrante: Jens Stoye, Bielefeld University, Germany
Local: UFF, Campus GRAGOATÁ
Sala: 407, Bloco H, 4o. andar
Horário: 16h

Título: Modeling and Finding Spatial Gene Clusters

Resumo: The search for common gene clusters within a set of genomes has been a central topic in computational comparative genomics for many years. The amount and size of groups of genes appearing closely together in the genomes of different species is a reliable measure for the degree of their relationship. Genes with a conserved neighborhood in various species' genomes can also give hints on an associated function or regulation.

To find such common gene clusters, a genome is often reduced to the order of its genes which are represented as a sequence of characters where homologous genes are represented by the same character. In this context, a common gene cluster is a set of genes that are co-located in the sequences of at least two genomes. Based on this representation, several mathematical models for gene clusters and algorithms to find them have been introduced during the last 20 years. All of them take into account the one-dimensional gene order in the genomic sequence without considering any spatial information regarding the three-dimensional structure of the chromatid in the cell.

We present for the first time a model that includes information about the spatial structure of the genomes to the gene cluster model. While an exponential time algorithm can simply be derived, it was so far impossible to find an exact algorithm working in polynomial time. On the other hand, it is open whether the problem is NP-hard.

Observações: This is joint work with Tizian Schulz. O professor Jens Stoye é professor visitante da Pós-graduação da Matemática - IME UFF - através do projeto PVE/Ciência sem Fronteiras/CAPES coordenado pela professora Simone Dantas.

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