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Nucleic Acids Research, 2003, Vol. 31, No. 13 3510-3517
© 2003 Oxford University Press

Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence

Yvonne J. K. Edwards*, Tim J. Carver, Tanya Vavouri, Martin Frith, Martin J. Bishop and Greg Elgar

Comparative Genomics Group, Research Division, MRC UK Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK

*To whom correspondence should be addressed. Tel: +44 1223494531; Fax: +44 1223494512; Email: yjedward{at}hgmp.mrc.ac.uk

Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences. A case study using the p53 promoter region of four mammalian species and two fish species is described. Unlike the mammalian sequences the promoter regions in fish have not been previously predicted or characterized and we report the differences in the p53 promoter region of four mammals and that predicted for two fish species. Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/.


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