Kerepesi Csaba, Szalkai Balázs, Grolmusz Vince
PIT Bioinformatics Group, Eötvös University, Pázmány Péter stny 1/c, 1117, Budapest, Hungary,
Microb Ecol. 2015 Apr;69(3):695-7. doi: 10.1007/s00248-014-0502-6. Epub 2014 Oct 10.
Low-cost DNA sequencing methods have given rise to an enormous development of metagenomics in the past few years. One basic--and difficult--task is the phylogenetic annotation of the metagenomic samples studied. The difficulty comes from the fact that the typical environmental sample contains hundreds of unknown and still uncharacterized microorganisms. There are several possible methods to assign at least partial phylogenetic information to these uncharacterized data. Originally, the 16S ribosomal RNA was used as phylogenetic marker, then genome sequence alignments and similarity measures between the unknown genome and the reference genomes were applied (e.g., in the MEGAN software), and more recently, phylogeny-based methods applying suitable sets of marker genes were suggested (AMPHORA, AMPHORA2, and the webserver implementation AmphoraNet). Here, we present a visual analysis tool that is capable of demonstrating the quantitative relations gained from the output of the AMPHORA2 program or the easy-to-use AmphoraNet webserver. Our web-based tool, the AmphoraVizu webserver, makes the phylogenetic distribution of the metagenomic sample clearly visible by using the native output format of AMPHORA2 or AmphoraNet. The user may set the phylogenetic resolution (i.e., superkingdom, phylum, class, order, family, genus, and species) along with the chart type and will receive the distribution data detailed for all relevant marker genes in the sample. For publication quality results, the chart labels can be customized by the user. The visualization webserver is available at the address http://amphoravizu.pitgroup.org. The AmphoraNet webserver is available at http://amphoranet.pitgroup.org. The open-source version of the AmphoraVizu program is available for download at http://pitgroup.org/apps/amphoravizu/AmphoraVizu.pl.
在过去几年中，低成本的DNA测序方法推动了宏基因组学的巨大发展。一项基本且困难的任务是对所研究的宏基因组样本进行系统发育注释。困难源于这样一个事实，即典型的环境样本包含数百种未知且尚未表征的微生物。有几种可能的方法可将至少部分系统发育信息赋予这些未表征的数据。最初，16S核糖体RNA被用作系统发育标记，随后应用了未知基因组与参考基因组之间的基因组序列比对和相似性度量（例如在MEGAN软件中），最近，有人提出了应用合适的标记基因集的基于系统发育的方法（AMPHORA、AMPHORA2以及网络服务器实现版本AmphoraNet）。在此，我们展示一种可视化分析工具，它能够展示从AMPHORA2程序或易于使用的AmphoraNet网络服务器的输出中获得的定量关系。我们基于网络的工具AmphoraVizu网络服务器，通过使用AMPHORA2或AmphoraNet的原始输出格式，使宏基因组样本的系统发育分布清晰可见。用户可以设置系统发育分辨率（即超界、门、纲、目、科、属和种）以及图表类型，并将收到样本中所有相关标记基因的详细分布数据。为了获得可用于发表的高质量结果，图表标签可由用户定制。可视化网络服务器的网址为http://amphoravizu.pitgroup.org。AmphoraNet网络服务器的网址为http://amphoranet.pitgroup.org。AmphoraVizu程序的开源版本可从http://pitgroup.org/apps/amphoravizu/AmphoraVizu.pl下载。
