The RAST Server: Rapid Annotations using Subsystems Technology

Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
BMC Genomics (Impact Factor: 3.99). 02/2008; 9(1):75. DOI: 10.1186/1471-2164-9-75
Source: PubMed


The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.
We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service.
By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

158 Reads
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    • "For mapping, we required 97% sequence identity over 100% of the read length, and exported results as BAM files. We used RAST (Aziz et al., 2008) and myRAST (available from for functional characterization of contigs. "
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    ABSTRACT: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
    PeerJ 10/2015; 3(358):e1319. DOI:10.7717/peerj.1319 · 2.11 Impact Factor
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    • "Contigs were ordered against reference genomes using CONTIGuator v2.7.3 (Galardini et al., 2011) and gaps were closed where possible using IMAGE (Tsai, Otto & Berriman, 2010) within the PAGIT wrapper v1.64 (Swain et al., 2012). Genomes were submitted to RAST for annotation (Aziz et al., 2008). Draft assemblies were compared with reference genomes using progressiveMauve (Darling, Mau & Perna, 2010). "
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    ABSTRACT: The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.
    PeerJ 09/2015; 3(23):e1223. DOI:10.7717/peerj.1223 · 2.11 Impact Factor
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    • "Using P4C2 sequencing chemistry, DNA sequencing was performed using Pacific Biosciences (PacBio) RSII sequencer in four Single Molecule Real Time (SMRT) cells. The resulting 217.24 fold coverage sequencing reads were then de novo assembled using Hierarchical Genome Assembly Process (HGAP) algorithm version 3. The assembled GC-rich (53.60 %) single circular contig of 6,000,511 bp (Table 1) was functionally annotated with NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.10, PROKKA pipeline (Seemann, 2014) and Rapid Annotation using Subsystem Technology (RAST) version 2.0 (Aziz et al., 2008). Additionally, a local BLASTP run was carried in search of genes of interest. "
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    ABSTRACT: Here, we present the first complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting (PGP) bacterium which confers solubilization of inorganic phosphate, indole-3-acetic acid production, hydrogen cyanideproduction, siderophore production and assimilation of ammonia through the glutamate synthase (GS/GOGAT) pathway. This genome sequence is valuable for functional genomics and ecological studies which are related to PGP and biocontrol activities.
    Journal of Biotechnology 09/2015; 214. DOI:10.1016/j.jbiotec.2015.09.005 · 2.87 Impact Factor
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