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      The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

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          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.

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          Most cited references 9

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          tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

           T. M. Lowe,  S. Eddy (1997)
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            IMG 4 version of the integrated microbial genomes comparative analysis system

            The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).
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              CDD: a conserved domain database for interactive domain family analysis

              The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of ‘Conserved Domain’ links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at . Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.
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                Author and article information

                Contributors
                mhuntemann@lbl.gov
                Journal
                Stand Genomic Sci
                Stand Genomic Sci
                Standards in Genomic Sciences
                BioMed Central (London )
                1944-3277
                26 October 2015
                26 October 2015
                2015
                : 10
                Affiliations
                [ ]Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA
                [ ]Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
                [ ]Present Address: Computational Biology Group, Celgene Corporation, Summit, USA
                Article
                77
                10.1186/s40793-015-0077-y
                4623924
                26512311
                © Huntemann et al. 2015

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Categories
                Standard Operating Procedure
                Custom metadata
                © The Author(s) 2015

                Genetics

                microbial genome annotation, sop, img, jgi

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