External Services

The NMPDR includes the following additional web sites.

Rapid Annotation using Subsystem Technology (RAST)

RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree.

As the number of more or less complete bacterial and archaeal genome sequences is constantly rising, the need for high quality automated initial annotations is rising with it. In response to numerous requests for a SEED-quality automated annotation service, we provide RAST as a free service to the community. It leverages the data and procedures established within the SEED framework to provide automated high quality gene calling and functional annotation. RAST supports both the automated annotation of high quality genome sequences AND the analysis of draft genomes. The service normally makes the annotated genome available within 12-24 hours of submission.

Meta Genome - RAST

The metagenomics RAST server is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly.

Annotation Clearinghouse

The Annotation Clearinghouse is a rather simple web site that collects Assertions about proteins and allows users to retrieve them. If you give the clearinghouse the ID of a protein or a ProteinEncodingGene (e.g., tr|Q40XE9, uni|Q40XE9, fig|266940.1.peg.3572, gi|69288893, NP_251014, kegg|pae:PA2324, or sp|Q03224), the server will return IDs of other proteins it knows about that have the same sequence. Furthermore, associated with each ID will be the function asserted for that ID by the major annotation teams that use that ID (at least those for which we can download their annotations). Thus, at any point where you have an ID, you can quickly get opinions about that protein (or other proteins that have the same sequence).