Ribosomal RNA (rRNA) sequences are central to biology from both the basic and the methodological perspectives. As the key elements in the cellular translation process they are worthy of detailed structure/function studies in their own right. In addition, their "evolutionary characteristics" make them extremely useful as tools in a number of other areas, microbiology in particular. Comparative analysis of rRNA sequences has (1) provided the secondary structure of the rRNAs themselves; (ii) led to the inference of the universal tree of life--a basis for a natural microbial classification--and the discovery of the Archaea; (iii) provided the basis for new and powerful approaches to microbial ecology; (iv) defined targets for much of the "probe" development in medical diagnosis; and (v) provided new methods for environmental impact and bioremediation assessment. All such studies require large amounts of rRNA data, and these can be used effectively only in the context of the appropriate database of rRNA sequences; one that not only provides the raw sequence data, but also organizes the data into alignments, provides a phylogenetic overview, makes available programs for data handling and analysis, and (for many users) offers a suite of services to assist them in their handling and analysis of the data. In that an rRNA sequence database this useful, this versatile, did not exist, the Ribosome Database Project (RDP) has been established at the University of Illinois (with a grant from NSF). Through its E-mail and FTP servers, the RDP offers aligned and phylogenetically ordered rRNA sequences in a variety of user-selected formats, as well as various software for handling and analysis of data. In addition, services such as automated sequence alignment, probe design checking, user-selected subsets of the sequence data and phylogenetic trees, and rRNA secondary structures are provided. Major objectives of this proposal are: (i) provide current alignments of rR NA data; (ii) provide a phylogenetic tree for those data; (iii) further automate the internal data updating and data management procedures; (iv) develop a "next generation" sequence alignment editor; (v) improve and expand the sequence data handling and analysis tools, including those for probe development, sequence alignment, and phylogenetic analysis; (vi) add new and improved software and services to the RDP servers; (vii) add new forms of data access and distribution; and (viii) increase the types of ribosome-related sequence alignments offered. Given the present volume of rRNA sequence data (approximately 2000 sequences) and the estimated future level (some estimates running into the millions), the RDP has an essential role to play in biological, medical and environmental research in the future.
