基因组序列中结构化非编码RNA基序的从头发现。

De novo discovery of structured ncRNA motifs in genomic sequences.

作者信息

Ruzzo Walter L, Gorodkin Jan

机构信息

Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

出版信息

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15.

DOI:10.1007/978-1-62703-709-9_15

PMID:24639166

Abstract

De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.

摘要

从头发现能够捕捉相关非编码（ncRNA）结构化RNA之间共性的“基序”，是计算生物学中最具挑战性的问题之一。本章概述了该问题所带来的挑战，以及一些解决这些挑战的方法，并重点以基于CMfinder程序的方法作为案例进行研究。文中还介绍了其在新型从头结构化ncRNA基因组筛选中的应用，包括蛋白质编码基因非翻译区中的结构化RNA元件。