16S rRNA Database

Query the SIMO Database

Overview

All information about samples, clones, 16S gene sequences, and other SIMO research products is organized in a relational database management system. The database model was designed to reflect the natural hierarchy that exists among samples and information and materials derived from them, and to maintain the complete research context for data stored in the system (view database diagram). Referential integrity constraints, data dictionaries, and list-based data entry applications are used to ensure the integrity and quality of all information stored in the database.

Scope

The SIMO database is primarily designed for archival, synthesis, and distribution of data from SIMO research to the microbial ecology community. However, information derived from analysis of 16S sequences using standard bioinformatics tools, such as the Ribosomal Database Project's Sequence Match program and sequence alignment tools in the FASTA package, is stored in the database to provide taxonomic context. Additional information about SIMO taxonomic methodology and RDPquery, an end-user Java program for classifying 16S rRNA sequences, are available on the Bacterial Taxonomy page. Various sequence formatting options are also provided to facilitate use of SIMO data with other databases and applications.

Access

SIMO participants can access the full database for data entry, querying, and administration using a combination of private web applications and custom database interface programs. Other researchers can access portions of the database to look up specific 16S rRNA sequences or search for sequences by taxonomic characteristics or ecological characteristics of the original sample.

Publications

The design and structure of the SIMO 16S rRNA database are described in more detail in the following publication:

Sheldon, W.M., M.A. Moran and J.T. Hollibaugh. 2002. Efforts to link ecological metadata with bacterial gene sequences at the Sapelo Island Microbial Observatory. Proceedings of the 6th World Multiconference on Systemics, Cybernetics, and Informatics -- Information Systems Development II. VII:402-407. (Adobe Acrobat® version, PowerPoint® presentation).