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The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes |
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| Authors: | Mavromatis Konstantinos Ivanova Natalia N Chen I-Min A Szeto Ernest Markowitz Victor M Kyrpides Nikos C |
| Institution: | 1Genome Biology Program, Department of Energy Joint Genome Institute, Walnut Creek, California, USA;2Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA |
| 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 (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence 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. |
| Keywords: | Joint Genome Institute gene prediction functional annotation GeneMark Metagene tRNA-Scan RNAmmer Rfam IMG-ER |
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