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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

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Product type Paperback
Published in Nov 2018
Publisher Packt
ISBN-13 9781789344691
Length 360 pages
Edition 2nd Edition
Languages
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Table of Contents (12) Chapters Close

Preface 1. Python and the Surrounding Software Ecology FREE CHAPTER 2. Next-Generation Sequencing 3. Working with Genomes 4. Population Genetics 5. Population Genetics Simulation 6. Phylogenetics 7. Using the Protein Data Bank 8. Bioinformatics Pipelines 9. Python for Big Genomics Datasets 10. Other Topics in Bioinformatics 11. Advanced NGS Processing

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 at the National Center for Biotechnology Information (NCBI). We will not only discuss GenBank, but also other databases at 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...

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