ESTIMA, a tool for EST management in a multi-project environment

Background: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. Results: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple highthroughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. Thes...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Charu G. Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A. Lewin, Lei Liu
• Keywords: Annotation, BMCBI 2004, ESTIMA, ESTs