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The RAST Server: Rapid Annotations using Subsystems Technology
TLDR
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. Expand
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
TLDR
The interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources are described. Expand
The RDP-II (Ribosomal Database Project)
TLDR
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. Expand
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
TLDR
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. Expand
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
TLDR
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. Expand
The RDP (Ribosomal Database Project)
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically orderedExpand
A new version of the RDP (Ribosomal Database Project)
TLDR
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. Expand
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
TLDR
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. Expand
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 ribosomalExpand
The Ribosomal Database Project.
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically orderedExpand
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