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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
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
The genetic data environment an expandable GUI for multiple sequence analysis
An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is basedExpand
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
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
TLDR
The sequencing and analysis of the type strain B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables the comparative analysis to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers. Expand
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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