DNA Property plot
This unit is devised to build profile of DNA conformational or physico-chemical properties. User may choose any of the 38 dinucleotide parameter sets and specify the averaging window size to construct a profile for a DNA sequence of interest. Each proposed parameter set represents an experimentally defined or theoretically calculated context-dependent DNA property. Different averaging sliding window sizes designed to perform profile smoothing.
Firstly position-specific dinucleotide frequencies for DNA sequence are computed. Than sliding window applied to calculate profiles of averaged dinucleotide frequencies. Finally DNA property plot calculation performed by dinucleotide frequencies profiles and the specified set of dinucleotide parameters. These parameters conform to chosen DNA conformational or physico-chemical property.
The source sample of DNA sequences in (ATGC or atgc) alphabet should be presented as a single string per sequence without any delimiters within the sequence.
The sequence length could not exceed 32kbp.
Program Property plot will be used for various DNA pattern revealing.