Subsystems-based servers for rapid annotation of genomes and metagenomes
© Aziz; licensee BioMed Central Ltd. 2010
Published: 23 July 2010
Today, more than 1000 genomes of cellular organisms, mostly microbes, have been completely sequenced and deposited in public databases, in addition to over 2000 viral genomes, and these numbers are expected to skyrocket in the near future. While sequencing projects remain largely biased towards genomes linked to human interests  (e.g., domestic animals and plants, microbial pathogens, and microbes exploited in industry and agriculture), some serious initiatives are being launched for sequencing organisms that represent all branches of the tree of life .
Concomitant with the genomic revolution, unprecedented advances in sequencing technology have also led to the emergence of the field of metagenomics, which offers a novel, revolutionary approach for studying (microscopic) life in different environments. Metagenomics allows investigators to assess the biodiversity in a given ecosystem by directly sequencing DNA sampled from that ecosystem [3–5]. As so-called next-generation sequencing technologies evolve, producing tremendous amounts of data , the existing tools for sequence annotation are not fast enough to cope with the technological advances. Consequently, manual annotation has almost become impossible; however, automated annotation tools often lead to error propagation and biologically irrelevant ontologies.
Materials and methods
Here, I demonstrate how the use of the subsystems  and FIGfams [8, 9] technologies, initiated by the Fellowship for Interpretation of Genomes (FIG) and the University of Chicago National Microbial Pathogen Data Resource (NMPDR) project , has improved the accuracy and consistency of genome and metagenome annotation . Using subsystems allows the combination of careful human annotation and the rapid computational propagation of assertions made by human experts through the RAST  pipeline for genome annotation, the MG-RAST server for metagenome annotation , and Phage-RAST for phage genome annotation (work in progress).
Results and conclusion
Still, although these servers offer relatively rapid annotation, the increasing throughput of sequencing platforms requires even faster pipelines, and annotating a large metagenomic data set can take weeks to months. To address this challenge, researchers at San Diego State University, FIG, and the Argonne National Laboratory are developing a protein family signature-based technology (Robert A. Edwards, Ross Overbeek, et al. submitted) to reduce the annotation speed by an order of magnitude and create a real-time annotation server (URL: http://edwards.sdsu.edu/rtmg). Such server will not only improve speed, but will allow the implementation of annotation pipelines on cell phones (Josh Hoffman et al., unpublished data) and social networks (Daniel Cuevas et al., unpublished data).
I thank Dr. Robert A. Edwards for sharing details about work in progress performed in his laboratory (URL: http://edwards.sdsu.edu/labsite) at San Diego State University, San Diego, CA, USA.
- Aziz RK: The case for biocentric microbiology. Gut Pathog 2009, 1: 16. 10.1186/1757-4749-1-16PubMed CentralView ArticlePubMedGoogle Scholar
- Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al.: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462: 1056–1060. 10.1038/nature08656PubMed CentralView ArticlePubMedGoogle Scholar
- Riesenfeld CS, Schloss PD, Handelsman J: Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004, 38: 525–552. 10.1146/annurev.genet.38.072902.091216View ArticlePubMedGoogle Scholar
- Handelsman J: Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004, 68: 669–685. 10.1128/MMBR.68.4.669-685.2004PubMed CentralView ArticlePubMedGoogle Scholar
- Edwards RA, Rohwer F: Viral metagenomics. Nat Rev Microbiol 2005, 3: 504–510. 10.1038/nrmicro1163View ArticlePubMedGoogle Scholar
- Schuster SC: Next-generation sequencing transforms today's biology. Nat Methods 2008, 5: 16–18. 10.1038/nmeth1156View ArticlePubMedGoogle Scholar
- Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33: 5691–5702. 10.1093/nar/gki866PubMed CentralView ArticlePubMedGoogle Scholar
- Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al.: The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9: 75. 10.1186/1471-2164-9-75PubMed CentralView ArticlePubMedGoogle Scholar
- Meyer F, Overbeek R, Rodriguez A: FIGfams: yet another set of protein families. Nucleic Acids Res 2009, 37: 6643–6654. 10.1093/nar/gkp698PubMed CentralView ArticlePubMedGoogle Scholar
- McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, et al.: The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res 2007, 35: D347–353. 10.1093/nar/gkl947PubMed CentralView ArticlePubMedGoogle Scholar
- Overbeek R, Bartels D, Vonstein V, Meyer F: Annotation of bacterial and archaealgenomes: improving accuracy and consistency. Chem Rev 2007, 107: 3431–3447. 10.1021/cr068308hView ArticlePubMedGoogle Scholar
- Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al.: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9: 386. 10.1186/1471-2105-9-386PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd.