NeSSie：一种用于识别近似 DNA 序列对称性的工具。

NeSSie: a tool for the identification of approximate DNA sequence symmetries.

机构信息

Department of Molecular Medicine, University of Padova, Padova, Italy.

出版信息

Bioinformatics. 2018 Jul 15;34(14):2503-2505. doi: 10.1093/bioinformatics/bty142.

DOI:10.1093/bioinformatics/bty142

PMID:29522153

Abstract

MOTIVATION

Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures.

RESULTS

We developed NeSSie, an easily customizable C/C++ 64-bit library and tool, based on dynamic programming, to quickly scan for perfect and degenerate DNA palindromes, mirrors and potential triplex forming patterns. In addition, the tool computes linguistic complexity and Shannon entropy measures to verify the repetitive nature of the DNA regions enriched in these motifs. As a case study, the analysis of the Mycobacterium bovis genome is presented.

AVAILABILITY AND IMPLEMENTATION

http://www.medcomp.medicina.unipd.it/main_site/doku.php? id=nessie and https://github.com/B3rse/nessie.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

非 B 型 DNA 构象在基因组重排、结构三维组织和基因调控中发挥着重要作用。许多非 B 型 DNA 结构表现出作为回文和镜像的对称特性，可形成发夹、十字形结构或三联体。为了进一步研究可能形成非 B 型 DNA 结构的核苷酸片段，我们需要一种能够快速在全基因组范围内搜索精确和简并对称模式的综合工具。