From Gene Annotation to Function Prediction for Metagenomics

Methods in Molecular Biology
Fatemeh Sharifi, Yuzhen Ye

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 .

Citations

Dec 2, 2017·Nucleic Acids Research·Chengsheng ZhuYana Bromberg
Feb 24, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bojan BozicMarko Djordjevic

Related Concepts

Sequence Determinations, DNA
Metagenome
Metagenomics
Molecular Sequence Annotation
Genes
Research
Enzyme Activity
Analysis
Gene Ontology
Nucleic Acid Sequencing

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