The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

By Marcel Huntemann, Natalia N. Ivanova, K. Mavromatis, H. J. Tripp, David Páez-Espino, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati and 3 more. Standards in Genomic Sciences, 2015

308 citations recorded by the source corpus.

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

Subfields: Endocrinology, Molecular Biology, Plant Science

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In Molecular Biology

1. S. Hung
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Citations in the corpus

• CRISPRDetect: A flexible algorithm to define CRISPR arrays (2016, unknown): “4 [56, 57] and NCBI [58]).”
• Genomes OnLine Database (GOLD) v.8: overview and updates (2020, background): “Well-defined genome and metagenome projects in GOLD are a prerequisite for sub-mitting sequence data to the Integrated Microbial Genomes with Microbiome (IMG / M) (17) system for annotation and analysis (18,19).”
• Growth enhancement and drought tolerance of hybrid poplar upon inoculation with endophyte consortia (2016, methodology): “7 endophyte strains were sequenced by the Joint Genome Institute (JGI) and were annotated using JGI’s microbial annotation pipeline [46].”