More on GC content and how it is calculated in ‘windows’
In this short video, we will review the concept of GC content and calculation using windows. We will also show a short demonstration in Artemis.
We can calculate the percentage of Gs and Cs present in a genome. This will be calculated as the number of Gs + number of Cs divided by the total number of bases.
When calculating the GC content for a whole genome, this value takes only one figure and is a characteristic of some genomes. We say that some genomes are GC rich (that means high GC content) while others are GC poor (with low GC content).
However, the GC content is not the same along the whole genome. In fact, we observe that there are some regions where there seems to be higher concentration of Gs and Cs. We can systematically calculate the GC content in blocks of the genome that we call windows (as shown in the first part of the current video). In this process, a whole genome is divided into pieces and the GC content is calculated for each piece. We can then plot the changes in the GC content as the values for each of the blocks.
We can change the length of the blocks to have more or less resolution in the GC content.
Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis
Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis
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