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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Protein sequence analysis

We have already seen the recipe for a general sequence analysis (both for nucleic acids and proteins) in the previous chapter. However, while doing a protein sequence alignment, we can directly fetch the sequence data from PDB (www.rcsb.org) and do the alignment within the program in R. Furthermore, the position of a protein multiple sequence alignment plays an important role, and color is often used to indicate amino acid properties to aid in judging the conservation of a given amino acid substitution. This will ultimately affect the structural, functional, and physicochemical properties of proteins. Here, we will present a recipe to create such an alignment and coloring of alignment with a protein sequence alignment ...

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