Gene and translation initiation site prediction in metagenomic sequences

By Doug Hyatt, P. LoCascio, Loren J. Hauser, E. Uberbacher. Bioinform., 2012

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The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice (2019, methodology): “3) was used for gene prediction of metagenomic contigs (40).”
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, methodology): “Protein sequences were predicted for each contig using Prodigal [81, 82] with the “meta” procedure (−p meta).”
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, methodology): “60 (Hyatt et al. 2012) and Pfam (Finn et al.”
A practical guide to amplicon and metagenomic analysis of microbiome data (2020, background): “shtml Provides rapid prokaryotic genome annotation, calls metaProdigal (Hyatt et al., 2012) for metagenomic gene prediction.”
Machine learning for metagenomics: methods and tools (2015, methodology): “MetaProdigal (Hyatt et al., 2012) is a method that improves on the Prodigal software Hyatt et al.”