使用美国国立医学图书馆的比较基因组浏览器（CGV）对真核生物全基因组比对进行交互式可视化。

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

作者信息

Rangwala Sanjida H, Rudnev Dmitry V, Ananiev Victor V, Asztalos Andrea, Benica Barrett, Borodin Evgeny A, Bouk Nathan, Evgeniev Vladislav I, Kodali Vamsi K, Lotov Vadim, Mozes Eyal, Oh Dong-Ha, Omelchenko Marina V, Savkina Sofya, Sukharnikov Ekaterina, Virothaisakun Joël, Murphy Terence D, Pruitt Kim D, Schneider Valerie A

机构信息

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.

出版信息

bioRxiv. 2023 Nov 29:2023.10.30.564672. doi: 10.1101/2023.10.30.564672.

DOI:10.1101/2023.10.30.564672

PMID:38077029

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10705539/

Abstract

We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expose large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

摘要

我们报告了一种用于分析全基因组组装比对的新可视化工具——比较基因组浏览器（CGV）（https://ncbi.nlm.nih.gov/genome/cgv/）。CGV使用我们和其他人开发的组装比对算法，可视化由NCBI提供的同物种和跨物种的成对比对。研究人员可以使用两种不同的视图检查两个组装之间的比对：基于染色体带型的视图或二维基因组点图。全基因组比对视图揭示了跨越染色体的大结构差异，如倒位或易位。用户还可以导航到感兴趣的区域，在那里他们可以检测和分析特定染色体或基因区域内较小规模的缺失和重排。在可用的情况下，RefSeq或用户提供的基因注释会显示在带型视图中。CGV目前提供来自300多种动物、植物和真菌物种的约700个比对。CGV和相关的NCBI浏览器正在积极开发中，以进一步满足研究界在比较基因组可视化方面的需求。