Jaguc-a software package for environmental diversity analyses

Nebel M.E.; Wild S.; Holzhauser M.; Hüttenberger L.; Reitzig R.; Sperber M.; Stoeck T.

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Jaguc-a software package for environmental diversity analyses

机译：Jaguc-用于环境多样性分析的软件包

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The study of microbial diversity and community structures heavily relies on the analyses of sequence data, predominantly taxonomic marker genes like the small subunit of the ribosomal RNA (SSU rRNA) amplified from environmental samples. Until recently, the "gold standard" for this strategy was the cloning and Sanger sequencing of amplified target genes, usually restricted to a few hundred sequences per sample due to relatively high costs and labor intensity. The recent introduction of massive parallel tag sequencing strategies like pyrosequencing (454 sequencing) has opened a new window into microbial biodiversity research. Due to its swift nature and relatively low expense, this strategy produces millions of environmental SSU rDNA sequences granting the opportunity to gain deep insights into the true diversity and complexity of microbial communities. The bottleneck, however, is the computational processing of these massive sequence data, without which, biologists are hardly able to exploit the full information included in these sequence data. Results: The freely available standalone software package JAGUC implements a broad regime of different functions, allowing for efficient and convenient processing of a huge number of sequence tags, including importing custom-made reference data bases for basic local alignment searches, user-defined quality and search filters for analyses of specific sets of sequences, pairwise alignment-based sequence similarity calculations and clustering as well as sampling saturation and rank abundance analyses. In initial applications, JAGUC successfully analyzed hundreds of thousands of sequence data (eukaryote SSU rRNA genes) from aquatic samples and also was applied for quality assessments of different pyrosequencing platforms. Conclusions: The new program package JAGUC is a tool that bridges the gap between computational and biological sciences. It enables biologists to process large sequence data sets in order to infer biological meaning from hundreds of thousands of raw sequence data. JAGUC offers advantages over available tools which are further discussed in this manuscript.

机译：微生物多样性和群落结构的研究在很大程度上依赖于序列数据的分析，主要是从环境样品中扩增的生物分类标记基因，例如核糖体RNA（SSU rRNA）的小亚基。直到最近，该策略的“金标准”还是扩增靶基因的克隆和Sanger测序，由于相对较高的成本和劳动强度，通常限制为每个样品几百个序列。最近引入的大规模并行标签测序策略（如焦磷酸测序（454测序））为微生物多样性研究开辟了新窗口。由于其快速的性质和相对较低的费用，该策略可产生数百万条环境SSU rDNA序列，从而有机会深入了解微生物群落的真正多样性和复杂性。但是，瓶颈在于这些海量序列数据的计算处理，没有这些瓶颈，生物学家几乎无法利用这些序列数据中包含的全部信息。结果：可免费获得的独立软件包JAGUC实现了各种功能的广泛机制，从而可以高效便捷地处理大量序列标签，包括导入用于基本本地比对搜索，用户定义的质量和搜索过滤器，用于分析特定的序列集，基于成对比对的序列相似性计算和聚类，以及采样饱和度和秩丰度分析。在最初的应用中，JAGUC成功地分析了来自水生样品的数十万个序列数据（真核SSU rRNA基因），还被用于不同焦磷酸测序平台的质量评估。结论：新的程序包JAGUC是弥合计算科学与生物科学之间鸿沟的工具。它使生物学家能够处理大型序列数据集，以便从成千上万的原始序列数据中推断出生物学意义。 JAGUC提供了优于可用工具的优势，本手册将对此进行进一步讨论。

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《Journal of Bioinformatics and Computational Biology》 |2011年第6期|共25页
作者
Nebel M.E.; Wild S.; Holzhauser M.; Hüttenberger L.; Reitzig R.; Sperber M.; Stoeck T.;
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正文语种 eng
中图分类细胞生物学;
关键词
Environmental diversity analyses; microbial diversity; sequence data; software tools;

机译：环境多样性分析;微生物多样性;序列数据;软件工具;

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1. Jaguc-a software package for environmental diversity analyses [J] . Nebel M.E., Wild S., Holzhauser M., Journal of Bioinformatics and Computational Biology . 2011,第6期

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2. Statistical Software Applications and Review: The Single-Case Data Analysis Package: Analysing Single-Case Experiments with R Software [J] . Isis Bulté, Patrick Onghena Journal of Modern Applied Statistical Methods . 2013,第2期

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4. Evaluating Software Diversity in Branch Prediction Analyses for static WCET Estimation [C] . Joachim Fellmuth, Jonas Zell, Sabine Glesner IEEE International Conference on Embedded and Real-Time Computing Systems and Applications . 2019

机译：在静态WCET估计的分支预测分析中评估软件多样性
5. The external social networks of software designers: An empirical study of their association with the features and quality of microcomputer software packages [D] . Inouye, Alan Scott 1997

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6. Analysing the Zenith Tropospheric Delay Estimates in On-line Precise Point Positioning (PPP) Services and PPP Software Packages [O] . Jorge Mendez Astudillo, Lawrence Lau, Yu-Ting Tang, 2018

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7. : "This paper deals with the functionality of the flaked stone assemblages from several Neolithic sites of the NE of the Iberian Peninsula. The chronological framework ranges from the mid-6th to the mid-4th millennium cal. BCE, which corresponds to the Early and Middle Neolithic. This long period ranges from the arrival of the first farming communities in the Iberian Peninsula, around 5600-5500 cal. BCE, to 3600-3500 cal. BCE, two millennia later, when Neolithic communities had stably occupied most of the available territory, from the mountainous areas of the Pyrenees to the coastal areas of the Mediterranean.In this context, the NE of the Iberian Peninsula is one of the areas where a major number of use-wear analyses have been carried out, especially for what concerns the Neolithic period. This is mainly due to the interest shown by the directors of the excavations and by the Spanish use-wear specialists as well; both participated and cooperated in order to enlarge the number of contexts studied, making the NE of the Iberian Peninsula one of the areas of Europe with the largest number of ‘functional studies’. As a result, today we have a reliable picture of the type of lithic tools used by the first farming groups, how they were used, and which needs they were satisfying.The methodology employed for this type of analysis is today broadly shared by most use-wear specialists. A stereoscopic microscope is used together with a reflected-light microscope for the analysis of the archaeological specimens. Afterwards, the observed use-wear traces are compared with the traces from experimental tools. This study primarily made use of the tools preserved at the ‘Traceoteque’ of the Institución Milà y Fontanals of the CSIC of Barcelona.This paper presents the results obtained for the different types of analysed sites and the relative lithic assemblages. In this way, tools from different contexts are compared: open-air sites, caves and rock-shelters, pit-sites, burials, and mining sites. Such a diversity of contexts allowed for the exploration of the existence of recurrences and differences in the functionality of the lithic tools from one site to another. The results obtained have also provided information on some aspects related to the economic processes carried out at the different sites, caves, rock-shelters and open-air contexts. It has been possible to gain fresh data on the types of tasks carried out and their relative importance for each site, their relation with the geographical and environmental context and the natural resources available there. In addition, analysing tools recovered from burials – mainly individual inhumations – provided information on the relationships between the buried individuals and the working tools, in particular exploring the relationships between sex and age patterns and the types of tools deposited as goods.In conclusion, use-wear analysis allowed for the exploration of a variety of issues; from technical aspects related to the production and management of the lithic resources to social aspects related to the subsistence activities and the individuals that carried them out." [O] . Gibaja Bao, Juan Francisco, Mazzucco, Niccolo 2015

机译：：“本文研究了伊比利亚半岛东北部几个新石器时代遗址的片状石材组合的功能。时间框架从公元前6世纪中叶到4世纪中叶，分别对应于早期和早期。新石器时代中期，这段时间的长短是从伊比利亚半岛的第一个农业社区到来，大约在公元前5600-5500 cal，到了两千年后的3600-3500 BCE，当时新石器时代的社区稳定地占据了大部分可用土地。从比利牛斯山脉山区到地中海沿岸地区。在这种情况下，伊比利亚半岛东北部是进行过大量使用磨损分析的地区之一，尤其是在关注方面新石器时代，这主要是由于发掘负责人和西班牙使用服装专家表现出的浓厚兴趣；他们参与和合作以扩大孔蒂的数量xts进行了研究，使伊比利亚半岛的NE成为“功能研究”数量最多的欧洲地区之一。结果，今天我们可以可靠地了解第一批耕作小组使用的石器工具的类型，使用方法以及它们满足的需求。今天，大多数使用方法广泛共享用于这种类型的分析的方法穿专家。立体显微镜与反射光显微镜一起用于分析考古样本。然后，将观察到的使用磨损痕迹与实验工具的痕迹进行比较。这项研究主要利用了巴塞罗那CSIC的米拉·丰塔纳尔研究所的“ Traceoteque”中保存的工具。本文介绍了针对不同类型的分析地点和相对石器组合所获得的结果。通过这种方式，可以比较来自不同环境的工具：露天场所，洞穴和岩石避难所，露天场所，埋葬场所和采矿场所。如此多样的上下文允许探索重复性的存在以及从一个站点到另一个站点的石器工具的功能差异。所获得的结果还提供了与在不同地点，洞穴，避难所和露天环境中进行的经济过程有关的某些方面的信息。可以获得有关所执行任务的类型及其对每个站点的相对重要性，它们与地理和环境环境以及那里可用自然资源的关系的新数据。此外，对从墓葬中回收的工具（主要是个人遗体）进行分析，可提供有关被掩埋的个体与工作工具之间关系的信息，尤其是探索性别与年龄模式之间的关系以及作为商品存放的工具的类型。磨损分析允许探索各种问题；从与石器资源的生产和管理有关的技术方面到与自给活动及其实施者有关的社会方面。”

Jaguc-a software package for environmental diversity analyses

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