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Fractal visualisation of genomic sequences

by Sam Roberts

 

03 Nov 2008

Code covered by BSD License  

Visualise n-mer nucleotide sequences using a fractal visualisation based on a Sierpinski gasket.

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Description

Genomic researchers are often interested in counts of the nucleotide base in a genetic sequence. The Bioinformatics Toolbox contains functions for counting sequences of length one and two, ie individual bases and dimers. But there is currently no way of visualising counts of longer sequences. We turn to some work by Carr that advocates using a fractal visualisation, which is extensible (in theory) to arbitrarily long sequences.

Required Products Bioinformatics Toolbox
Statistics Toolbox
MATLAB release MATLAB 7.4 (R2007a)
Zip File Content  
Published M Files Fractal visualisation of genomic base counts
Other Files nmervis.m,
nmervisdemo.m,
nmervisdemo.png,
nmervisdemo_01.png,
nmervisdemo_02.png,
nmervisdemo_03.png,
nmervisdemo_04.png,
nmervisdemo_05.png
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Tag Applied By Date/Time
genetics Sam Roberts 03 Nov 2008 16:49:12
sequence analysis Sam Roberts 03 Nov 2008 16:49:12
bioinformatics Sam Roberts 03 Nov 2008 16:49:12
pharmaceutical Sam Roberts 03 Nov 2008 16:49:12
biotech Sam Roberts 03 Nov 2008 16:49:12
graphics Sam Roberts 03 Nov 2008 16:49:12
visualisation Sam Roberts 03 Nov 2008 16:49:12
visualization Sam Roberts 03 Nov 2008 16:49:12
fractal Sam Roberts 03 Nov 2008 16:49:12
 

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