NX4：一个基于网络的大型多重序列比对可视化工具。

NX4: a web-based visualization of large multiple sequence alignments.

机构信息

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

College of Arts, Media + Design, Northeastern University, Boston, MA 02115, USA.

出版信息

Bioinformatics. 2019 Nov 1;35(22):4800-4802. doi: 10.1093/bioinformatics/btz457.

DOI:10.1093/bioinformatics/btz457

PMID:31161215

Abstract

SUMMARY

Multiple Sequence Alignments (MSAs) are a fundamental operation in genome analysis. However, MSA visualizations such as sequence logos and matrix representations have changed little since the nineties and are not well suited for displaying large-scale alignments. We propose a novel, web-based MSA visualization tool called NX4, which can handle genome alignments comprising thousands of sequences. NX4 calculates the frequency of each nucleotide along the alignment and visually summarizes the results using a color-blind friendly palette that helps identifying regions of high genetic diversity. NX4 also provides the user with additional assistance in finding these regions with a 'focus + context' mechanism that uses a line chart of the Shannon entropy across the alignment. The tool offers geneticists an easy-to-use and scalable analysis for large MSA studies.

AVAILABILITY AND IMPLEMENTATION

NX4 is freely available at https://www.nx4.io, and its source code at https://github.com/NX4/nx4.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

多序列比对 (MSA) 是基因组分析的基本操作。然而，自 90 年代以来，序列标志和矩阵表示等 MSA 可视化方法几乎没有变化，不太适合显示大规模比对。我们提出了一种名为 NX4 的新型基于网络的 MSA 可视化工具，它可以处理包含数千个序列的基因组比对。NX4 计算沿比对的每个核苷酸的频率，并使用色盲友好的调色板直观地总结结果，有助于识别高度遗传多样性的区域。NX4 还通过使用对齐线上的香农熵折线图的“焦点+上下文”机制，为用户提供了查找这些区域的额外帮助。该工具为遗传学家提供了一种易于使用且可扩展的大型 MSA 研究分析方法。