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.