Improving A-GLAM for Finding DNA Regulatory Elements
Author Information
Author(s): Tharakaraman Kannan, Mariño-Ramírez Leonardo, Sheetlin Sergey L, Landsman David, Spouge John L
Primary Institution: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Hypothesis
Can the A-GLAM program be improved to more efficiently locate multiple occurrences of regulatory elements in DNA sequences?
Conclusion
The improvements to A-GLAM allow it to predict multiple instances of regulatory elements in DNA sequences more rapidly and accurately.
Supporting Evidence
- A-GLAM correctly identified 15 out of 19 known binding sites in histone promoters without any false positives.
- A-GLAM identified 5 out of 6 operator sites in lambda phage, missing only one.
- A-GLAM correctly identified 13 out of 14 Gal4p binding sites in yeast.
- A-GLAM identified 12 out of 27 Kruppel-binding sites in Drosophila without false positives.
Takeaway
This study made a computer program better at finding important parts of DNA by allowing it to look for many copies of these parts at once, instead of just one.
Methodology
The study improved the A-GLAM program by adding a scanning step after Gibbs sampling to locate multiple instances of regulatory elements in DNA sequences.
Limitations
The performance of A-GLAM may degrade on datasets with many repeat elements, which can overwhelm the detection of true regulatory signals.
Digital Object Identifier (DOI)
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