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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Getting the detail of a sequence composition

Once we have retrieved a sequence, we need to know more about it; for example, we need to know the nucleotide or amino acid frequency, and Guanine and Cytosine nucleotide bases (GC content). To illustrate, if we have repetitive bases, say, AAAAAA, the sequence is not very interesting because of low information content. The contents of a sequence also help in determining certain properties of the entire molecule, for example, the acid basicity hydrophobicity in proteins based on the amino acids present in the sequence.

An interesting aspect is the GC content in a nucleotide. It refers to the fraction of Guanine (G) and Cytosine (C) in the sequence, and certain genomes, especially among the bacteria, show ...

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