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A-GAME：提高汇集功能宏基因组序列数据的组装质量。

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

机构信息

Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.

出版信息

BMC Genomics. 2018 Jan 12;19(1):44. doi: 10.1186/s12864-017-4369-z.

DOI:10.1186/s12864-017-4369-z
PMID:29329522
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5767027/
Abstract

BACKGROUND

Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications.

RESULTS

Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation.

CONCLUSION

In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame.

摘要

背景

环境 DNA（eDNA）文库的表达筛选是一种鉴定和描述具有潜在生物技术特性的新型微生物酶的常用方法。在这种“功能宏基因组学”实验中，基于活性测定选择的插入片段通过高通量测序技术进行测序。组装后进行基因预测、注释和候选基因的鉴定，然后对候选基因进行生物技术应用评估。

结果

在这里，我们介绍了 A-GAME（用于功能宏基因组学的 GAlaxy 套件），这是一个网络服务，包含用于分析 eDNA 序列数据的最先进的工具和工作流程。我们使用真实的功能宏基因组学数据说明了 A-GAME 工作流程的潜力，表明它们优于替代的宏基因组组装程序。A-GAME 中提供的专用工具允许对混合库进行有效的分析，并快速鉴定候选基因，从而降低测序成本并节省繁琐的手动注释的需要。

结论

总之，我们相信 A-GAME 将成为功能宏基因组学社区的宝贵资源。A-GAME 可在 http://beaconlab.it/agame 上公开获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/7e723d99e3b1/12864_2017_4369_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/c37aa50e0840/12864_2017_4369_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/c586dd6970e1/12864_2017_4369_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/7e723d99e3b1/12864_2017_4369_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/c37aa50e0840/12864_2017_4369_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/c586dd6970e1/12864_2017_4369_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/025c/5767027/7e723d99e3b1/12864_2017_4369_Fig3_HTML.jpg

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