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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Retrieving a sequence from UniProt

To begin with the protein analyses, we first need to retrieve a protein sequence. UniProt is a high-quality and freely accessible database of protein sequences and functional information. It should be noted that certain other databases such as RefSeq also provide protein sequence information, but UniProt is a manually curated one and hence better for analytical purposes in this recipe. We use this as the source for our sequence information. This recipe will explain a few ways to retrieve sequences from UniProt using R.

Getting ready

Retrieving sequences from the UniProt database simply requires an identification of the protein sequence that we want to retrieve. We will look for the NAD kinase (NADK) enzyme in humans ...

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