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Bioinformatics with Python Cookbook
Tiago Antao
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eBook - ePub
Bioinformatics with Python Cookbook
Tiago Antao
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Information
Bioinformatics with Python Cookbook
Table of Contents
Bioinformatics with Python Cookbook
Credits
About the Author
About the Reviewers
www.PacktPub.com
Support files, eBooks, discount offers, and more
Why Subscribe?
Free Access for Packt account holders
Preface
What this book covers
What you need for this book
Who this book is for
Sections
Getting ready
How to do it…
There's more…
See also
Conventions
Reader feedback
Customer support
Downloading the example code
Downloading the color images of this book
Errata
Piracy
Questions
1. Python and the Surrounding Software Ecology
Introduction
Installing the required software with Anaconda
Getting ready
How to do it…
There's more…
See also
Installing the required software with Docker
Getting ready
How to do it…
See also
Interfacing with R via rpy2
Getting ready
How to do it…
There's more…
See also
Performing R magic with IPython
Getting ready
How to do it…
See also
2. Next-generation Sequencing
Introduction
Accessing GenBank and moving around NCBI databases
Getting ready
How to do it…
There's more…
See also
Performing basic sequence analysis
Getting ready
How to do it…
There's more…
See also
Working with modern sequence formats
Getting ready
How to do it…
There's more…
See also
Working with alignment data
Getting ready
How to do it…
There's more…
See also
Analyzing data in the variant call format
Getting ready
How to do it…
There's more…
See also
Studying genome accessibility and filtering SNP data
Getting ready
How to do it…
There's more…
See also
3. Working with Genomes
Introduction
Working with high-quality reference genomes
Getting ready
How to do it...
There's more...
See also
Dealing with low-quality genome references
Getting ready
How to do it...
There's more...
See also
Traversing genome annotations
Getting ready
How to do it...
There's more...
See also
Extracting genes from a reference using annotations
Getting ready
How to do it…
There's more...
See also
Finding orthologues with the Ensembl REST API
Getting ready
How to do it...
There's more...
Retrieving gene ontology information from Ensembl
Getting ready
How to do it...
There's more...
See also
4. Population Genetics
Introduction
Managing datasets with PLINK
Getting ready
How to do it…
There's more...
See also
Introducing the Genepop format
Getting ready
How to do it…
See also
Exploring a dataset with Bio.PopGen
Getting ready
How to do it…
There's more...
See also
Computing F-statistics
Getting ready
How to do it…
See also
Performing Principal Components Analysis
Getting ready
How to do it…
There's more...
See also
Investigating population structure with Admixture
Getting ready
How to do it…
There's more...
5. Population Genetics Simulation
Introduction
Introducing forward-time simulations
Getting ready
How to do it...
There's more...
Simulating selection
Getting ready
How to do it…
There's more...
Simulating population structure using island and stepping-stone models
Getting ready
How to do it…
Modeling complex demographic scenarios
Getting ready
How to do it…
Simulating the coalescent with Biopython and fastsimcoal
Getting ready
How to do it…
There's more...
See also
6. Phylogenetics
Introduction
Preparing the Ebola dataset
Getting ready
How to do it...
There's more...
See also
Aligning genetic and genomic data
Getting ready
How to do it...
Comparing sequences
Getting ready
How to do it...
There's more…
Reconstructing phylogenetic trees
Getting ready
How to do it...
There's more...
Playing recursively with trees
Getting ready
How to do it...
There's more...
Visualizing phylogenetic data
Getting ready
How to do it...
There's more...
7. Using the Protein Data Bank
Introduction
Finding a protein in multiple databases
Getting ready
How to do it...
There's more...
Introducing Bio.PDB
Getting ready
How to do it...
There's more...
Extracting more information from a PDB file
Getting ready
How to do it...
Computing molecular distances on a PDB file
Getting ready
How to do it...
Performing geometric operations
Getting ready
How to do it...
There's more...
Implementing a basic PDB parser
Getting ready
How to do it...
There's more...
Animating with PyMol
Getting ready
How to do it...
There's more...
Parsing mmCIF files using Biopython
Getting ready
How to do it...
There's more...
8. Other Topics in Bioinformatics
Introduction
Accessing the Global Biodiversity Information Facility
How to do it...
There's more...
Geo-referencing GBIF datasets
Getting ready
How to do it...
There's more...
Accessing molecular-interaction databases with PSIQUIC
How to do it...
Plotting protein interactions with Cytoscape the hard way
Getting ready
How to do it...
There's more...
9. Python for Big Genomics Datasets
Introduction
Setting the stage for high-performance computing
Getting ready
How to do it...
Designing a poor human concurrent executor
Getting ready
How to do it...
There's more...
Performing parallel computing with IPython
Getting ready
How to do it...
There's more...
Computing the median in a large dataset
Getting ready
How to do it...
There's more...
Optimizing code with Cython and Numba
Getting ready
How to do it...
There's more...
Programming with laziness
Getting ready
How to do it...
There's more...
Thinking with generators
Getting ready
How to do it...
See also
Index
Bioinformatics with Python Cookbook
Copyright © 2015 Packt Publishing
All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without the prior written permission of the publisher, except in the case of brief quotations embedded in critical articles or reviews.
Every effort has been made in the preparation of this book to ensure the accuracy of the information presented. However, the information contained in this book is sold without warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers and distributors will be held liable for any damages caused or alleged to be caused directly or indirectly by this book.
Packt Publishing has endeavored to provide trademark information about all of the companies and products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot guarantee the accuracy of this information.
First published: June 2015
Production reference: 1230615
Published by Packt Publishing Ltd.
Livery Place
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Birmingham B3 2PB, UK.
ISBN 978-1-78217-511-7
www.packtpub.com
Credits
Author
Tiago Antao
Reviewers
Cho-Yi Chen
Giovanni M. Dall'Olio
Commissioning Editor
Nadeem N. Bagban
Acquisition Editor
Kevin Colaco
Content Development Editor
Gaurav Sharma
Technical Editor
Shashank Desai
Copy Editor
Relin Hedly
Project Coordinator
Harshal Ved
Proofreader
Safis Editing
Indexer
Monica Ajmera Mehta
Production Coordinator
Arvindkumar Gupta
Cover Work
Arvindkumar Gupta
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