Discovering geometric patterns in genomic data

Abstract

ChIP-chip and ChIP-seq are techniques for the isolation and identification of the binding sites of DNA-associated proteins along the genome. Both techniques produce genome-wide location data. The geometric arrangements of these binding sites can provide valuable information about biological function, such as the activation or repression of genes.In this paper, we formalize this problem and propose a novel graph based algorithm called Patterns of Marks (PoM) to discover efficiently these types of geometric patterns in genomic data. We also describe how we validate the algorithm using experimental data.

Searching for patterns of association between functional genomic elements

“…После нахождения распределения плотностей хромосом в гене, для каждого из файлов был реализован алгоритм [6] для дальнейшего поиска корреляции между двумя аннотациями.…”