PRISM: A New Method for Identifying Cis-Regulatory Elements
Author Information
Author(s): Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross
Primary Institution: University of Washington
Hypothesis
Can a new algorithm effectively identify degenerate cis-regulatory elements in DNA sequences?
Conclusion
The PRISM algorithm outperforms existing motif finders in identifying degenerate cis-regulatory elements.
Supporting Evidence
- PRISM consistently outperformed nine other motif finders on 28 well-characterized S. cerevisiae regulons.
- The algorithm requires no tunable parameters, making it user-friendly.
- PRISM's performance was validated against experimentally characterized binding sites.
Takeaway
PRISM is a computer program that helps scientists find important DNA sequences that control gene activity, and it does this better than other programs.
Methodology
PRISM identifies overrepresented motifs and iteratively relaxes them into degenerate motifs without tunable parameters.
Potential Biases
The algorithm's performance may be affected by the presence of noise in the input sequences.
Limitations
PRISM may not work well for cis-regulatory elements with widely spaced critical residues.
Statistical Information
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website