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Others: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome

TitleAQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome
Authors
KeywordsMetagenome
Metatranscriptome
Absolute quantification
Differential expression genes
Issue Date2017
Citation
bioRxiv, 2017, article no. 218347 How to Cite?
AbstractMetatranscriptome has become increasingly important along with the application of next generation sequencing in the studies of microbial functional gene activity in environmental samples. However, the quantification of target active gene is hindered by the current relative quantification methods, especially when tracking the sharp environmental change. Great needs are here for an easy-to-perform method to obtain the absolute quantification. By borrowing information from the parallel metagenome, an absolute quantification method for both metagenomic and metatranscriptomic data to per gene/cell/volume/gram level was developed. The effectiveness of AQMM was validated by simulated experiments and was demonstrated with a real experimental design of comparing activated sludge with and without foaming. Our method provides a novel bioinformatic approach to fast and accurately conduct absolute quantification of metagenome and metatranscriptome in environmental samples. The AQMM can be accessed from https://github.com/biofuture/aqmm.
DescriptionThis article is a preprint and has not been certified by peer review.
Persistent Identifierhttp://hdl.handle.net/10722/293562

 

DC FieldValueLanguage
dc.contributor.authorJiang, X-
dc.contributor.authorYu, K-
dc.contributor.authorLi, L-
dc.contributor.authorYin, X-
dc.contributor.authorLi, A-
dc.contributor.authorZhang, T-
dc.date.accessioned2020-11-23T08:18:35Z-
dc.date.available2020-11-23T08:18:35Z-
dc.date.issued2017-
dc.identifier.citationbioRxiv, 2017, article no. 218347-
dc.identifier.urihttp://hdl.handle.net/10722/293562-
dc.descriptionThis article is a preprint and has not been certified by peer review.-
dc.description.abstractMetatranscriptome has become increasingly important along with the application of next generation sequencing in the studies of microbial functional gene activity in environmental samples. However, the quantification of target active gene is hindered by the current relative quantification methods, especially when tracking the sharp environmental change. Great needs are here for an easy-to-perform method to obtain the absolute quantification. By borrowing information from the parallel metagenome, an absolute quantification method for both metagenomic and metatranscriptomic data to per gene/cell/volume/gram level was developed. The effectiveness of AQMM was validated by simulated experiments and was demonstrated with a real experimental design of comparing activated sludge with and without foaming. Our method provides a novel bioinformatic approach to fast and accurately conduct absolute quantification of metagenome and metatranscriptome in environmental samples. The AQMM can be accessed from https://github.com/biofuture/aqmm.-
dc.languageeng-
dc.relation.ispartofbioRxiv-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectMetagenome-
dc.subjectMetatranscriptome-
dc.subjectAbsolute quantification-
dc.subjectDifferential expression genes-
dc.titleAQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome-
dc.typeOthers-
dc.identifier.emailLi, L: liliguan@hku.hk-
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hk-
dc.identifier.authorityZhang, T=rp00211-
dc.description.naturepreprint-
dc.identifier.doi10.1101/218347-
dc.identifier.hkuros319375-
dc.identifier.spagearticle no. 218347-
dc.identifier.epagearticle no. 218347-

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