title: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).
abstract: The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA ; Present Address: Computational Biology Group, Celgene Corporation, Summit, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: H James
authors.initials: HJ
authors.lastname: Tripp
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: David
authors.initials: D
authors.lastname: Paez-Espino
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Krishnaveni
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: I-Min A
authors.initials: IM
authors.lastname: Chen
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: Torben
authors.initials: T
authors.lastname: Nielsen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
keywords: IMG; JGI; Microbial Genome Annotation; SOP