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Stand Genomic Sci. 2009 Jul 20;1(1):63-7. doi: 10.4056/sigs.632.

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes.


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.


GeneMark; IMG-ER; Joint Genome Institute; Metagene; RNAmmer; Rfam; functional annotation; gene prediction; tRNA-Scan

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