Department of Molecular Medicine, University of Padova, Padova, Italy.
Bioinformatics. 2018 Jul 15;34(14):2503-2505. doi: 10.1093/bioinformatics/bty142.
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.
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.
http://www.medcomp.medicina.unipd.it/main_site/doku.php? id=nessie and https://github.com/B3rse/nessie.
Supplementary data are available at Bioinformatics online.
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。
我们开发了 NeSSie，这是一个基于动态编程的、易于定制的 C/C++ 64 位库和工具，用于快速搜索完美和简并的 DNA 回文、镜像和潜在的三联体形成模式。此外，该工具还计算语言复杂度和香农熵度量，以验证富含这些基序的 DNA 区域的重复性质。作为案例研究，我们展示了对牛分枝杆菌基因组的分析。
http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=nessie 和 https://github.com/B3rse/nessie。
补充数据可在生物信息学在线获得。
