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

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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.