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From Gene Annotation to Function Prediction for Metagenomics

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1611)

Abstract

Microbes play important roles in almost every aspect of life, including human health and diseases. Facilitated by the rapid development of sequencing technologies, metagenomics research has accelerated the accumulation of genomic sequences of microbial species that had been inaccessible before. Analysis of the metagenomic sequencing data can reveal not only the species but also the functional composition of microbial communities. Here, we report a pipeline for functional annotation of metagenomic datasets. The pipeline is built from several programs that we have developed for metagenomic sequence analysis including a protein-coding gene predictor for short reads (or contigs) and a fast similarity search tool. Given a metagenomic dataset, the pipeline reports putative protein-coding genes (or gene fragments) and functional annotations of the genes in Gene Ontology (GO) terms and Enzyme Commission (EC) numbers, and potential metabolic pathways that are likely encoded by the metagenome. Fun4Me is available for download at https://sourceforge.net/projects/fun4me.

Keywords

Metagenomics Similarity search Function prediction Gene Ontology (GO) Metabolic pathway 
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Notes

Acknowledgments

This work was supported by NIH grant 1R01AI108888 and NSF grant DBI-0845685.

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© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.School of Informatics and ComputingIndiana UniversityBloomingtonUSA

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