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

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

Figure 1

Data flow for gene prediction in the DOE-JGI MAP. Nucleotide sequences are annotated using tools to predict repeats (CRISPR) and RNA genes. Subsequently protein-coding genes are predicted using either GeneMark or Metagene. The consolidated results are then used to create a Genbank file, which is uploaded into the IMG/ER database.

Figure 2

The gene product name assignment procedure used in the DOE-JGI MAP. Genes are first compared to protein families (COGs, Pfam, TIGRfam) and protein databases (KEGG, IMG). A product name is assigned through a series of checks to identify significant hits to IMG terms and the protein families databases. At the end of the process translation tables are used to produce a Genbank compliant product name from the respective source.