MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes

BMC Biology

Software

Josh D. Neufeld¹  Daniel A. Kurtz¹  Pavel Petrenko¹  Andrew C. Doxey¹  Briallen Lobb¹ 

[1] Department of Biology, University of Waterloo, 200 University Ave. West, N2L 3G1, Waterloo, ON, Canada;

关键词: Metagenomics;    Microbiome;    Next-generation sequencing;    Taxonomic profiling;   

DOI  :  10.1186/s12915-015-0195-4

 received in 2015-07-06, accepted in 2015-10-02,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundMetagenomes provide access to the taxonomic composition and functional capabilities of microbial communities. Although metagenomic analysis methods exist for estimating overall community composition or metabolic potential, identifying specific taxa that encode specific functions or pathways of interest can be more challenging. Here we present MetAnnotate, which addresses the common question: “which organisms perform my function of interest within my metagenome(s) of interest?” MetAnnotate uses profile hidden Markov models to analyze shotgun metagenomes for genes and pathways of interest, classifies retrieved sequences either through a phylogenetic placement or best hit approach, and enables comparison of these profiles between metagenomes.ResultsBased on a simulated metagenome dataset, the tool achieves high taxonomic classification accuracy for a broad range of genes, including both markers of community abundance and specific biological pathways. Lastly, we demonstrate MetAnnotate by analyzing for cobalamin (vitamin B12) synthesis genes across hundreds of aquatic metagenomes in a fraction of the time required by the commonly used Basic Local Alignment Search Tool top hit approach.ConclusionsMetAnnotate is multi-threaded and installable as a local web application or command-line tool on Linux systems. Metannotate is a useful framework for general and/or function-specific taxonomic profiling and comparison of metagenomes.

【 授权许可】

CC BY   
© Petrenko et al. 2015