A new bioinformatic resource: A heterotrimeric G-protein database (hGPDB).

摘要

Bioinformatics is the computer-assisted analysis, management, and manipulation of data related to biological systems. We have created a bioinformatic web-based resource to enhance research in heterotrimeric G-protein mediated signal transduction, a ubiquitous process that regulates many cellular functions. This resource facilitates analysis of existing physical and biological information as well as the formulation of hypotheses for further research and experimentation. A large amount of information relevant to heterotrimeric G-protein mediated signal transduction exists. Our database offers advantages that include dramatic decreases in the retrieval time of specified datatypes and access to information otherwise beyond electronic analysis.; Our heterotrimeric G-protein database is designed and developed to accommodate large amounts of data linked by complex relationships. Through the use of web pages and programs written in JAVA, the contents of the database are accessible using a web browser. In formulating conceptual and logical data models for the database, we identified a number of data entities and relationships needed to generate a minimum virtual representation of heterotrimeric G-protein mediated signal transduction. These objects and relationships were then incorporated into the physical programming and implementation of the database. In addition to the development of the database and a web application to access it, a desk top JAVA utility was written to facilitate the retrieval of the database's information from public sources. Utilities to update, delete, or add information to the underlying database were constructed. We integrated a sequence alignment algorithm into the web application that allows users to align protein sequences. We enhanced the alignment output by adding color-coding. In addition to the interactive pages and tools that allow controlled access and queries to the database, users can view static web pages with information, links, and references related to heterotrimeric G-proteins. The database is constructed to be flexible and scalable, able to evolve and increase in utility with additional information and functionalities. We are the first to achieve the physical implementation of data, application, and presentation client-server layers essential for a functional web-based database focused on heterotrimeric G-protein mediated signal transduction.