Bioinformatics with Python cookbook : learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology / Tiago Antao.
- 1st edition
- Birmingham, England ; Mumbai, [India] : Packt Publishing, 2015.
- Community experience distilled.
Community Experience Distilled
1 online resource (306 p.)
- Python (Computer program language).
- Electronic books.
- System Details:
- text file
- If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.
- Cover; Copyright; Credits; About the Author; About the Reviewers; www.PacktPub.com; Table of Contents; Preface; Chapter 1: Python and the Surrounding Software Ecology; Introduction; Installing the required software with Anaconda; Installing the required software with Docker; Interfacing with R via rpy2; Performing R magic with IPython; Chapter 2: Next-generation Sequencing; Introduction; Accessing GenBank and moving around NCBI databases; Performing basic sequence analysis; Working with modern sequence formats; Working with alignment data; Analyzing data in variant call format
Studying genome accessibility and filtering SNP dataChapter 3: Working with Genomes; Introduction; Working with high-quality reference genomes; Dealing with low-quality genome references; Traversing genome annotations; Extracting genes from a reference using annotations; Finding orthologues with the Ensembl REST API; Retrieving gene ontology information from Ensembl; Chapter 4: Population Genetics; Introduction; Managing datasets with PLINK; Introducing the Genepop format; Exploring a dataset with Bio.PopGen; Computing F-statistics; Performing Principal Components Analysis
Investigating population structure with AdmixtureChapter 5: Population Genetics Simulation; Introduction; Introducing forward-time simulations; Simulating selection; Simulating population structure using island and stepping-stone models; Modeling complex demographic scenarios; Simulating the coalescent with Biopython and fastsimcoal; Chapter 6: Phylogenetics; Introduction; Preparing the Ebola dataset; Aligning genetic and genomic data; Comparing sequences; Reconstructing phylogenetic trees; Playing recursively with trees; Visualizing phylogenetic data; Chapter 7: Using the Protein Data Bank
IntroductionFinding a protein in multiple databases; Introducing Bio.PDB; Extracting more information from a PDB file; Computing molecular distances on a PDB file; Performing geometric operations; Implementing a basic PDB parser; Animating with PyMol; Parsing mmCIF files using Biopython; Chapter 8: Other Topics in Bioinformatics; Introduction; Accessing the Global Biodiversity Information Facility; Geo-referencing GBIF datasets; Accessing molecular-interaction databases with PSIQUIC; Plotting protein interactions with Cytoscape the hard way; Chapter 9: Python for Big Genomics Datasets
IntroductionSetting the stage for high-performance computing; Designing a poor human concurrent executor; Performing parallel computing with IPython; Computing the median in a large dataset; Optimizing code with Cython and Numba; Programming with laziness; Thinking with generators; Index
- Includes index.
"Quick answers to common problems"--Cover.
Description based on online resource; title from PDF title page (ebrary, viewed July 11, 2015).
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