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The RAST Server: Rapid Annotations using Subsystems Technology
A fully automated service for annotating bacterial and archaeal genomes that 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.
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
The interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources are described.
The RDP-II (Ribosomal Database Project)
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. (2000), continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands.
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
A new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences, which is based on version 3.3 of Felsenstein's dnaml program and significantly improve performance and reduce memory usage, making it feasible to construct even very large trees.
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center, which provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace.
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
- D. Lane, B. Pace, G. Olsen, D. Stahl, M. Sogin, N. Pace
- BiologyProceedings of the National Academy of Sciences…
- 1 October 1985
A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16 S rRNA or cloning of its gene, and its phylogenetic usefulness is evaluated by examination of several 17S rRNAs whose gene sequences are known.
A new version of the RDP (Ribosomal Database Project)
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. (1997), is now hosted by the Center for Microbial Ecology at Michigan State University and will provide more rapid updating of data, better data accuracy and increased user access.
The ribosomal database project
The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal…
The RDP (Ribosomal Database Project)
- B. Maidak, G. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, C. Woese
- Biology, Computer ScienceNucleic Acids Res.
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered…