Abstract

The compilation of multiple metazoan genome sequences and the deluge of large-scale expression data have combined to motivate the maturation of bioinformatics methods for the analysis of sequences that regulate gene transcription. Historically, these bioinformatics methods have been plagued by poor predictive specificity, but new bioinformatics algorithms that accelerate the identification of regulatory regions are drawing disgruntled users back to their keyboards. However, these new approaches and software are not without problems. Here, we introduce the purpose and mechanisms of the leading algorithms, with a particular emphasis on metazoan sequence analysis. We identify key issues that users should take into consideration in interpreting the results and provide an online training example to help researchers who wish to test online tools before taking an independent foray into the bioinformatics of transcription regulation.

Author affiliations

1. Centre for Molecular Medicine and Therapeutics and British Columbia Women's and Children's Hospitals, 3018-950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, Canada.
2. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada.
3. Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, SE-171 77, Stockholm, Sweden.

Correspondence to: Wyeth W. Wasserman^1,2 Email: Wyeth@cmmt.ubc.ca

MORE ARTICLES LIKE THIS

These links to content published by NPG are automatically generated.