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Regular version of the site

Book chapter

Поиск паттернов ассоциации между функциональными элементами генома

С. 1-3.
Маткаримов О. О., Поливода Д. Э., Попцова М. С.

Next-generation sequencing technologies made it possible to map numerous functional genomic elements. Thus, it became possible to define positions of epigenetic factors including methylation, histone modifications, sites of open chromatin, regulatory RNA, and also binding sites for transcription factors and other important proteins. Data, generated as a result of NGS-experiments, are stored at the project web-sites and is freely available usually in bed-format. The problem of finding associations between different functional genomic annotations, both experimental and theoretical, is very important. The existing programs for pattern search have significant limitations. most of them are developed to work in the Unix-like systems, they are lacking graphical interface, and programs are complex in usage. In the present work we present a program that can be run in a browser in any operation system, it has a graphical interface, and it accepts as an input two files of genome annotations in .bed format, visualize distribution of functional elements as densities at the level of chromosome and performs a search for patterns of association between different functional genomic annotations. The detected patterns are visualized and information about their position is given in a list. The presented program is designed to solve a broad class of bioinformatics problems of finding patterns of association between different functional genome annotations.

In book

Т. 7. Пущино: Государственное учреждение Институт математических проблем биологии РАН, 2018.