title: Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.
abstract: 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/.
authors.affiliation: Comparative Genomics Group, Research Division, MRC UK Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK. yjedward@hgmp.mrc.ac.uk
authors.forename: Yvonne J K
authors.initials: YJ
authors.lastname: Edwards
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Carver
authors.forename: Tanya
authors.initials: T
authors.lastname: Vavouri
authors.forename: Martin
authors.initials: M
authors.lastname: Frith
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Bishop
authors.forename: Greg
authors.initials: G
authors.lastname: Elgar
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D003196:Computer Graphics; D006224:Cricetinae; D005399:Fishes / Q000235:genetics; D040461:Gene Components; D005786:Gene Expression Regulation; D016158:Genes, p53; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors