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On the Visualization of the DNA Sequence and its Nucleotide Content

Aleksandr Mylläri, Tapio Salakoski, Alexey Pasechnik, On the Visualization of the DNA Sequence and its Nucleotide Content. ACM SIGSAM Bulletin 39(4), 131 - 135, 2005.

Abstract:

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.

BibTeX entry:

@ARTICLE{jMySaPa05a,
  title = {On the Visualization of the DNA Sequence and its Nucleotide Content},
  author = {Mylläri, Aleksandr and Salakoski, Tapio and Pasechnik, Alexey},
  journal = {ACM SIGSAM Bulletin},
  volume = {39},
  number = {4},
  pages = {131 - 135},
  year = {2005},
}

Belongs to TUCS Research Unit(s): Algorithmics and Computational Intelligence Group (ACI)

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