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On the visualization of the DNA sequence and its nucleotide content

建立日期：2018/02/21
  • 作者： Aleksandr Myll¨ari等
  • 出處： 2006-04-13 Department of Information Technology
  • 內容： Visual inspection can help reveal patterns that would be computationally rather difficult to reveal.We consider three different algorithms for visualizations of a DNA sequence and its nucleotide content:random walk, fractal and visualization based on the entropy-like parameters calculated using a sliding window. We present a program that uses these three methods and visualizes either the whole of a given sequence, or specified fragments. It also provides facilities to compare visualizations obtained for different sequences/fragments.

    Random walk visualization considers the sequence symbol-by-symbol;the other two methods also take into account how well nucleotides are ”mixed” in the sequence.It allows an easy visualization of repeated patterns, segments with a high/low content of some nucleotides,such as CG-islands, etc. The program also helps to identify regions of interest for further study.

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