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Nucleic Acids Research 2005 33(Web Server Issue):W271-W273; doi:10.1093/nar/gki589
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Article

SVC: structured visualization of evolutionary sequence conservation

S. Roepcke*, P. Fiziev, P. H. Seeburg1 and M. Vingron

Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany 1Max Planck Institute for Medical Research Jahnstrasse 73, 69120 Heidelberg, Germany

*To whom correspondence should be addressed. Tel: +49 30 84131159; Fax: +49 30 84131152; Email: roepcke{at}molgen.mpg.de

Received February 14, 2005. Revised April 29, 2005. Accepted April 29, 2005.

We have developed a web application for the detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. Given a pair of orthologous genes, the protein-coding sequences are aligned. When these sequences are mapped back onto their encoding exons in the genomes, a scaffold of the conserved gene structure naturally emerges. Sequence similarity between exons and introns is analysed and embedded into the gene structure scaffold. The visualization on the SVC server provides detailed information about evolutionarily conserved features of these genes. It further allows concise representation of complex splice patterns in the context of evolutionary conservation. A particular application of our tool arises from the fact that around mRNA editing sites both exonic and intronic sequences are highly conserved. This aids in delineation of these sites. SVC is available at http://svc.molgen.mpg.de.


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