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EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries
Robin P Smith1, William J Buchser, Marcus B Lemmon
1The Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, USA. rsmith@med.miami.edu
BMC Bioinformatics
|April 12, 2008
Summary
EST Express is a new open-source web application for analyzing expressed sequence tags (ESTs) from cDNA libraries. It simplifies gene identification and annotation, aiding researchers in managing sequencing projects.
Area of Science:
- Bioinformatics
- Molecular Biology
- Genomics
Background:
- Functional cDNA sets require sequencing and analysis.
- Redundant databases (e.g., UniGene) and annotation engines (e.g., Entrez Gene) facilitate sequence analysis.
Purpose of the Study:
- To develop software for identifying and annotating expressed sequence tags (ESTs) from specific mRNA populations.
- To create a user-friendly tool for managing cDNA library sequencing projects and facilitating researcher collaboration.
Main Methods:
- Developed "EST Express", a suite of analytical tools with a graphical user interface (GUI) powered by PHP and MySQL.
- Integrated continuity with UniGene, Entrez Gene, and RefSeq databases.
- Implemented a novel Entrez Gene parser and project management tools for cDNA libraries.
Main Results:
- The software, EST Express, successfully identifies and annotates ESTs from specific mRNA populations.
- Tested on a dataset of 2,016 samples from subtractive hybridization, demonstrating its capability.
- Provides multiple layers of annotation using Entrez Gene and RefSeq for gene highlighting.
Conclusions:
- EST Express is an open-source, cross-platform web server application.
- Facilitates the import and analysis of sequences from various cDNA library types.
- Enables users to highlight useful genes and manage cDNA library projects effectively.
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