Abstract
restez: Create and Query a Local Copy of GenBank in R
Highlights
Downloading sequences and sequence information from GenBank (Benson et al, 2013) and related NCBI databases is often performed via the NCBI API, Entrez
We can download and create a local copy of the primates GenBank locally and re-run the above code with a library call to restez for speed-up gains and increased code reliability
With a good internet connection and a computer with currently standard capabilities, a database comprising 7 GB of sequence information (i.e. the total sequence data available for Rodentia as of 27 June 2018) can be generated in less than 10 minutes. (For an outline of the functions and structure of restez, see Figure 1.)
Summary
Downloading sequences and sequence information from GenBank (Benson et al, 2013) and related NCBI databases is often performed via the NCBI API, Entrez (J. Ostell, 2002). Downloading sequences and sequence information from GenBank (Benson et al, 2013) and related NCBI databases is often performed via the NCBI API, Entrez Entrez has a limit on the number of requests, downloading large amounts of sequence data in this way can be inefficient. Entrez limits the number of entries that can be retrieved at once, requiring a user to develop code for querying in batches.
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