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Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(5):669-670; doi:10.1093/bioinformatics/bti030
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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 Road, Athens, GA 30602, USA
2 Janie Pumphrey 2028 Spruce St Apt 3R, Philadelphia, PA 19103, USA

*To whom correspondence should be addressed.

Summary: ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are 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 to sequence data, GenBank records or 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

Contact: agingle{at}uga.edu


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[Abstract] [Full Text] [PDF]


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