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It has been observed that most monocot genes (with experimentally confirmed gene models) have
a negative gradient of GC content starting with the start codon (Wong et al., 2002). This
phenomenon has been observed in multiple monocots and is absent in all dicots studied. The
change in GC content is mainly a function of the wobble position of monocot codons. As a result,
the 5' end of monocot genes can have up to 25% higher GC content than the 3' end (Yu et al., 2002).
These gradients have not been reported in Arabidopsis, which has an average GC content of 43%
throughout the genic regions (Yu et al., 2002).
geneGC calculates the GC content within a specified window across any genomic, cDNA, mRNA sequence.
The output is in a form of a chart plotting the information provided and the actual numbers to import
into MS Excel or other graphing programs. Window size refers to the number of bases for which the GC content
will be calculated at each step. Step size is how many bases the window size will move forward at each step.
It is important to make the window and step size multiples of 3 to avoid codon bias. For example, the
default settings will calculate the GC content of the first 129 bases in the sequence then move forward
51 bases and calculate the GC content of bases 52-180.
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