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Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence
Yvonne J K Edwards1, Tim J Carver, Tanya Vavouri
1Comparative 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
Nucleic Acids Research
|June 26, 2003
Summary
Theatre is a web-based system for comparative genomic sequence analysis, aiding gene expression regulation studies. It reveals patterns in DNA sequences, including transcription factor binding sites, and presents findings for easy understanding.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Comparative genomic sequence analysis is crucial for understanding gene regulation.
- Identifying motifs involved in gene expression requires specialized tools.
- Existing tools may not offer integrated analysis of diverse sequence families.
Purpose of the Study:
- To introduce Theatre, a web-based system for comparative genomic sequence analysis.
- To facilitate the prediction of regulatory elements like transcription factor binding sites.
- To enable the visualization of sequence patterns across multiple species.
Main Methods:
- Theatre integrates common sequence analysis tools and biological databases.
- It analyzes DNA sequence families to identify coding regions, repetitive sequences, and transcription factor binding sites.
- The system provides web-based output and publication-quality hardcopies.
Main Results:
- Theatre successfully predicted features in aligned genomic sequences.
- A case study highlighted differences in the p53 promoter region between mammalian and fish species.
- The system revealed patterns not easily discernible through other methods.
Conclusions:
- Theatre is an effective tool for comparative genomic analysis and gene regulation studies.
- It enhances the discovery of sequence patterns and regulatory elements.
- The system provides valuable insights into evolutionary differences in promoter regions.