Software

WebScipio: An online tool for the determination of gene structures using protein sequences

Florian Odronitz¹ , Holger Pillmann¹ , Oliver Keller² , Stephan Waack² and Martin Kollmar¹

¹Max-Planck-Institut für Biophysikalische Chemie, Abteilung NMR-basierte Strukturbiologie, Am Fassberg 11, 37077 Göttingen, Germany

²Universität Göttingen, Institut für Informatik, Lotzestr. 16-18, 37083 Göttingen, Germany

author email corresponding author email

BMC Genomics 2008, 9:422doi:10.1186/1471-2164-9-422

Published:	18 September 2008

Abstract

Background

Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches.

Results

WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs.

Conclusion

WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org webcite.