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Using DSP To Find Coding Regions in DNA Sequences

Using DSP To Find Coding Regions in DNA Sequences. Anna de Regt and Rio Akasaka. Background. Exons are coding regions of DNA DNA exhibits period-three behavior Frequency Domain methods Sliding window DFT Auto-regressive method Time Domain methods Second-order resonant filter

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Using DSP To Find Coding Regions in DNA Sequences

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  1. Using DSP To Find Coding Regions in DNA Sequences Anna de Regt and Rio Akasaka

  2. Background • Exons are coding regions of DNA • DNA exhibits period-three behavior Frequency Domain methods • Sliding window DFT • Auto-regressive method Time Domain methods • Second-order resonant filter • Average Magnitude Difference Function (AMDF)

  3. Working with C. elegans Caenorhabditis elegans Soil nematode of approx. 1mm length First multicellular organism to have its genome completely sequenced, first published in 1998. Our data is from WormBase F56F11.4a Chromosome III Did you know? C. elegans made news when it was discovered that specimens had survived the Space Shuttle Columbia disaster in February 2003.]

  4. Shifting Window Method • Fourier Transform the base sequences • Evaluate over an N-length window and then shift window • Take k=N/3

  5. x(n) H(z) y(n) Digital Filter Method • 733 times faster • Apply an antinotch filter at ω=2π/3

  6. The filter Notch filter as seen in fdatool

  7. Exploiting Strand Symmetry C H A R G A F F ’ S R U L E : DNA from any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases i.e. %A+T=%G+G

  8. Using a Single Filter • Optimize the parameters t and g in • Have them add up to 1

  9. Quadratic Window • Filter the high-frequency components out of each peak

  10. Acknowledgements • Grateful acknowledgement to Prof. Erik Cheever • Fox & Carreira. A Digital Signal Processing Method for Gene Prediction with Improved Noise Suppression • Vaidyanathan & Yoon. Digital filters for gene prediction applications • Vaidyanathan & Yoon. Gene and Exon Prediction using Allpass-based Filters • Anastassiou. DSP in Genomics: Processing and Frequency-Domain Analysis of Character Strings • Anastassiou. Frequency-domain analysis of biomolecular sequences. • Akhtar.Comparison of Gene and Exon Prediction Techniques for Detection of Short Coding Regions.

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