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 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.
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. It is a fast, lightweight, open source gene prediction tool which compares favorably with other existing gene prediction tools.
dupFinisher is software used to finish repeats in a genome with minimal human interaction. It can automatically detect repetitive regions, assemble each repeat individually using paired draft reads and finishing reads, check the quality of these subassemblies, create artificial joins for finished and properly assembled repeats and run automated gap closure scripts on unfinished subassemblies, which can be incorporated in to the next run of dupFinisher.