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Nucleic Acids Research 2004 32(Web Server Issue):W301-W304; doi:10.1093/nar/gkh478
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences

Jan Krüger, Alexander Sczyrba*, Stefan Kurtz1 and Robert Giegerich

Technische Fakultät, Universität Bielefeld, D-33594 Bielefeld, Germany and 1 Zentrum für Bioinformatik, Universität Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany

* To whom correspondence should be addressed. Tel: +49 521 106 2910; Fax: +49 521 106 6411; Email: asczyrba{at}techfak.uni-bielefeld.de

Received February 15, 2004; Revised April 8, 2004; Accepted May 3, 2004

e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable time, and makes this improved efficiency available as a web service. Our server hosts large collections of EST sequences (e.g. 4.1 million mouse ESTs of 1.87 Gb) in precomputed indexed data structures for efficient sequence comparison. The user can upload a genomic DNA sequence of interest and rapidly compare this to the complete collection of ESTs on the server. This delivers a mapping of the ESTs on the genomic DNA. The e2g web interface provides a graphical overview of the mapping. Alignments of the mapped EST regions with parts of the genomic sequence are visualized. Zooming functions allow the user to interactively explore the results. Mapped sequences can be downloaded for further analysis. e2g is available on the Bielefeld University Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/e2g/.

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