Bioinformatics with Python Cookbook - B32056_13 (for Raymond Rhine) by Unknown

Author:Unknown
Language: eng
Format: epub
Tags: Bioinformatics, Python, Language Models, AI
Publisher: Packt Publishing
Published: 2025-11-21T00:00:00+00:00

Chapter 8: Accessing Public Databases

Join our book community on Discord

https://packt.link/EarlyAccessCommunity

In this chapter, we will see how to access the tremendous volume of information from previous sequencing and genome annotation projects. We’ll cover how to get access to genomic, RiboNucleic Acid (RNA), and protein data.There is a wealth of public data sources available to bioinformaticians these days. The National Center for Biotechnology Information (NCBI) houses GenBank, RefSeq, and other key sequence data sources. It holds protein structural data, taxonomies, variant information, and scientific references as well - https://www.ncbi.nlm.nih.gov/ . It also houses Entrez - https://www.ncbi.nlm.nih.gov/search/, which provides a unified search across numerous NCBI databases.The UCSC Genome Database - https://genome.ucsc.edu/ houses a popular genome browser for major organisms, comparative genomics data, and tracks for regulatory elements, clinical variations, and more.Ensembl - https://www.ensembl.org/index.html?redirect=no - provides genomic data, annotations, and comparative genomics viewers for numerous organisms. It includes data on regulatory elements and gene expression patterns as well.The Protein Data Bank (PDB) and UniProt (Universal Protein Resource) hold a wealth of protein sequencesIn this chapter, we will learn about the sources of public data available for bioinformatics and look at tools to programmatically access this data.We will cover the following recipes in this chapter:

Accessing GenBank and navigating NCBI databases

Using the Sequence Read Archive

Using PDB and UniProt

Download

Copyright Disclaimer:
This site does not store any files on its server. We only index and link to content provided by other sites. Please contact the content providers to delete copyright contents if any and email us, we'll remove relevant links or contents immediately.