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泛基因组的Pan-Tetris交互式可视化工具

Pan-Tetris: an interactive visualisation for Pan-genomes.

作者信息

Hennig André, Bernhardt Jörg, Nieselt Kay

出版信息

BMC Bioinformatics. 2015;16 Suppl 11(Suppl 11):S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.

DOI:10.1186/1471-2105-16-S11-S3
PMID:26328606
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4547177/
Abstract

BACKGROUND

Large-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes.

RESULTS

We introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table. The main features of Pan-Tetris are a standard coordinate based presentation of multiple genomes complemented by easy to use tools compensating for algorithmic weaknesses in the pan-genome generation workflow. We demonstrate an application of Pan-Tetris to the pan-genome of Staphylococcus aureus.

CONCLUSIONS

Pan-Tetris is currently the only interactive pan-genome visualisation tool. Pan-Tetris is available from http://bit.ly/1vVxYZT.

摘要

背景

大规模基因组计划为微生物泛基因组分析铺平了道路。泛基因组描述了所研究物种或分类单元的所有成员共有的所有基因的总和。它们提供了一个框架，用于评估给定个体基因组集合的基因组多样性，此外还有助于整合基因预测和注释。泛基因组的计算通常是一项挑战，许多使用与全局比对无关方法的技术存在无法区分旁系同源基因和直系同源基因的风险。此外，考虑基因邻域的基于比对的方法通常需要对结果进行额外的人工整理。这非常耗时，而且到目前为止，还没有一种可视化工具能够提供用于泛基因组的交互式图形用户界面，以支持对泛基因组计算或直系同源基因注释进行整理。

结果

我们推出了Pan-Tetris，这是一个基于Java的交互式软件工具，它为在泛基因组表中直观检查基因出现情况提供了一种结构清晰且合适的方式。Pan-Tetris的主要特点是以基于标准坐标的方式呈现多个基因组，并辅以易于使用的工具，以弥补泛基因组生成工作流程中的算法缺陷。我们展示了Pan-Tetris在金黄色葡萄球菌泛基因组中的应用。

结论

Pan-Tetris是目前唯一的交互式泛基因组可视化工具。可从http://bit.ly/1vVxYZT获取Pan-Tetris。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/aa5c2bed8f2f/1471-2105-16-S11-S3-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/ecad121991d4/1471-2105-16-S11-S3-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/92a1657aaceb/1471-2105-16-S11-S3-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/49adefd84ee7/1471-2105-16-S11-S3-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/8b3bf8f3e57a/1471-2105-16-S11-S3-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/c28d7dfddd63/1471-2105-16-S11-S3-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/c53ee366ab99/1471-2105-16-S11-S3-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/aa5c2bed8f2f/1471-2105-16-S11-S3-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/ecad121991d4/1471-2105-16-S11-S3-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/92a1657aaceb/1471-2105-16-S11-S3-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/49adefd84ee7/1471-2105-16-S11-S3-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/8b3bf8f3e57a/1471-2105-16-S11-S3-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/c28d7dfddd63/1471-2105-16-S11-S3-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/c53ee366ab99/1471-2105-16-S11-S3-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c1b4/4547177/aa5c2bed8f2f/1471-2105-16-S11-S3-7.jpg

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