Standard Operating Procedure for the Annotations of Microbial Genomes by the Production Genomic Facility of the DOE JGI

Konstantinos Mavromatis, Natalia Ivanova, Amy Chen, Ernest Szeto, Victor Markowitz, Nikos C. Kyrpides

Abstract


The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome [1] (IMG) system. DOE-JGI MAP annotation is applied on nucleotide se-quence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes.

doi:10.4056/sigs.632



Keywords


Joint Genome Institute, gene prediction, functional annotation, GeneMark, Meta-gene, tRNA-Scan, RNAmmer, Rfam, IMG-ER

Full Text: PDF HTML

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

This article doi:10.4056/sigs.632 has been cited by 5 other articles:

Complete genome sequence of “Enterobacter lignolyticus” SCF1
DeAngelis et al.
Stand. Genomic Sci. 5(1) 69.
10.4056/sigs.2104875

Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera
Lukjancenko et al.
Microb Ecol 63(3) 651.
10.1007/s00248-011-9948-y

The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium
van de Vossenberg et al.
() no.
10.1111/j.1462-2920.2012.02774.x

The State of Standards in Genomic Sciences
Garrity
Stand. Genomic Sci. 5(3) 262.
10.4056/sigs.2515706

Metagenomic analysis of a stable trichloroethene-degrading microbial community
Brisson et al.
ISME J () .
10.1038/ismej.2012.15



Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.

Standards in Genomic Sciences is indexed in:

Sponsors of the Genomic Standards Consortium: