This method examines the distribution of nucleotides and groups within a sequence. The overall patterns of nucleotide composition in the sequence can be described by the %GC, GC-skew and AT-skew. You can plot the frequency of single bases, base pairs and base skew.
The Window value is the number of bases over which the composition is calculated. For example, to calculate the frequency of C in a window of 100 bases, GeneQuest would count the number of Cs within the given 100 bases and divide the sum by 100. Values are plotted at the window center. Wider windows smooth out transient effects; narrower windows allow some small peaks to show through.
GeneQuest plots values for all nucleotides 5’ to 3’ on the sense strand. The complement is not used, nor are wobble frequencies taken into account.
To change method parameters:
- Double click on the method name in the Method Curtain; or select the method display and then Analysis > Method Parameters.
- The default Window size, 100 bases, is optimal for sequences averaging about 2000 bp. Increase this number for larger sequences and decrease it for smaller sequences.
- Change the significance thresholds, if necessary. The significance thresholds for the bases have default settings of: A=0.233, C=0.253, G=0.272, T=0.242. These thresholds were chosen based on global frequency values for coding regions of the Escherichia coli genome.
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