Effects of Symmetry on Motif Discovery
Author Information
Author(s): Motlhabi Lala M., Stormo Gary D.
Primary Institution: Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
Hypothesis
The study investigates how the assumption of symmetry in motif discovery affects the accuracy of predicting DNA binding sites for transcription factors.
Conclusion
The study shows that commonly used motif-finding approaches often incorrectly model symmetric motifs, leading to higher false prediction errors, but alternative methods can improve accuracy.
Supporting Evidence
- The study demonstrates that asymmetric models are superior when the true binding site is asymmetric.
- When the true binding specificity is symmetric, commonly used methods can incorrectly infer asymmetry.
- Inaccurate motifs lead to lower sensitivity and specificity than correct symmetric models.
- The study provides criteria for determining the appropriate model for experimental datasets.
Takeaway
This study helps scientists understand that when looking for DNA binding sites, assuming symmetry can lead to mistakes, but using the right methods can fix those mistakes.
Methodology
The study used simulation studies to test different motif finding algorithms on both symmetric and asymmetric binding site data.
Limitations
The study primarily relies on simulation data, which may not fully capture the complexities of real biological systems.
Digital Object Identifier (DOI)
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