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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti030
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 25, 2004
Revised July 30, 2004
Accepted September 9, 2004

Article

ESTminer: a Web interface for mining EST contig and cluster databases

Yecheng Huang 1*, Janie Pumphrey 2, and Alan R. Gingle 1

1 Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd., Athens, GA 30602, USA
2 Janie Pumphrey, 2028 Spruce St Apt 3R, Philadelphia, PA 19103

* To whom correspondence should be addressed. E-mail: bioinfo{at}uga.edu.


  Abstract

Summary: ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or threshold number of members with the results displayed as color-coded tree nodes where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members with links that can be configured for sequence data, GenBank records, or other user configurable links. Also, the interface allows "queries within queries" where the result set of a query is further filtered by the subsequent query.

Availability: ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp.


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