2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2017

Noam Kaplan, Job Dekker. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature biotechnology, 31(12):1143-1147. 2013.

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Despite advances in DNA sequencing technology, assembly of complex genomes
remains a major challenge, particularly for genomes sequenced using short reads, 
which yield highly fragmented assemblies. Here we show that genome-wide in vivo
chromatin interaction frequency data, which are measurable with chromosome
conformation capture-based experiments, can be used as genomic distance proxies
to accurately position individual contigs without requiring any sequence overlap.
We also use these data to construct approximate genome scaffolds de novo.
Applying our approach to incomplete regions of the human genome, we predict the
positions of 65 previously unplaced contigs, in agreement with alternative
methods in 26/31 cases attempted in common. Our approach can theoretically bridge
any gap size and should be applicable to any species for which global chromatin
interaction data can be generated.