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Expressed Sequence Tags (ESTs)

Volume 533 of the series Methods in Molecular Biology pp 241-256

Date:

EST Databases and Web Tools for EST Projects

  • Yao-Qing ShenAffiliated withRobert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal
  • , Emmet O’BrienAffiliated withRobert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal
  • , Liisa KoskiAffiliated withRobert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal
  • , B. Franz LangAffiliated withRobert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal
  • , Gertraud BurgerAffiliated withRobert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal

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Abstract

This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices.

Key words

EST database design data processing annotation Web interface data submission