In this seminar, current topics of the Genome Informatics research group are presented.

(In dieser Veranstaltung wird in Vorträgen über aktuelle Themen aus der Forschung der Arbeitsgruppe Genominformatik berichtet.)

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Martin Mascher

Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows the de novo production of a genetically anchored, linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1-Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to different genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources and will enable the rapid and cost efficient establishment of powerful genomic information for many species.

An Overview of Genomic Distances Modeled with Indels
Marília D. V. Braga

The genomic distance typically describes the minimum number of large-scale mutations that transform one genome into another. Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e., positions and orientation of pieces of DNA, and number of chromosomes). In order to handle genomes with distinct contents, also insertions and deletions of pieces of DNA—named indels—must be allowed. Some extensions of the classical approaches lead to models that allow rearrangements and indels. In this work we introduce a new graph structure that gives a unified view of these approaches, present an overview of their results and point out some open problems related to them.

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