A Knowledge Base for Storage and Analysis of Expressed Sequence Tags (ESTs)

University Of Delaware, Newark DE

Investigators

Abstract

Expressed sequence tags (EST's), are short nucleotide sequences determined from the cDNA copy of mRNA in a given cell, tissue, organ, or organism. EST's are widely used and equally widely generated, providing information about gene identity, expression and distribution for a wide range of organisms. Although it is relatively easy to generate the sequence information of an EST, there are a number of problems associated with storing and using the information. The software platform proposed here integrates a database, a biological ontology, or structured language, and sequence analysis functions for an EST knowledge base. This knowledge base addresses three problems faced by a biologist: storage of the data, analysis and archiving of the results, and integration into a cumulative database. The system is designed to permit a typical biologist to install and operate it. In order to do this, the system will provide user-friendly interfaces for additon of sequences, automated running of assembly and analysis programs, a query and alert system for complex searches, and a data sharing arrangement for geographically separate laboratories to permit integration. As a prototype, a knowledge base on the chicken will be developed. This is particularly useful since the chicken is often used as a comparative species for contrasting with mammals such as mouse and human. In developing the system, a range of training opportunities will be offered to undergraduates, graduates and postdoctoral scientists.