Accessing GenBank and moving around NCBI databases

Although you may have your own data to analyze, you will probably need existing genomic datasets. Here, we will look at how to access such databases from NCBI. We will not only discuss GenBank but also other databases from NCBI. Many people refer (wrongly) to the whole set of NCBI databases as GenBank, but NCBI includes the nucleotide database and many others—for example, PubMed.

As sequencing analysis is a long subject and this book targets intermediate to advanced users, we will not be very exhaustive with a topic that is, at its core, not very complicated.

Nonetheless, it’s a good warm-up for the more complex recipes that we will see at the end of this chapter.

Getting ready

We will use Biopython, which you installed in Chapter 1, Python and the Surrounding Software Ecology. Biopython provides an interface to Entrez, the data retrieval system made available by NCBI.

This recipe is made available in the...