Book Image

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
Book Image

Bioinformatics with Python Cookbook

By: Tiago R Antao, Tiago Antao

Overview of this book

Table of Contents (16 chapters)
Bioinformatics with Python Cookbook
Credits
About the Author
About the Reviewers
www.PacktPub.com
Preface
Index

Index

A

  • admixture
    • URL / Investigating population structure with Admixture, Getting ready
    • population structure, investigating with / Getting ready, How to do it…, There's more...
  • aligned sequences
    • comparing / Comparing sequences, How to do it...
  • alignment data
    • working with / Working with alignment data, How to do it…, There's more…, See also
  • AmiGO
    • URL / See also
  • Anaconda
    • URL / Introduction, See also
    • used, for installing software / Installing the required software with Anaconda, Getting ready, How to do it…, See also
    • distribution, URL / How to do it…
  • animation
    • with PyMol / Animating with PyMol, How to do it..., There's more...
  • annotations
    • used, for extracting genes from reference / Extracting genes from a reference using annotations, How to do it…, There's more...
  • Anopheles genomes
    • URL / Getting ready
  • Arlequin
    • about / There's more…
    • URL / There's more…
  • arXiv
    • URL / See also
  • awkward variations
    • URL / There's more...

B

  • BED format
    • URL / See also
  • Bio.PDB
    • about / Introducing Bio.PDB
    • using / Getting ready, How to do it..., There's more...
  • Bio.Phylo
    • about / How to do it...
  • Bio.PopGen
    • used, for exploring dataset / Exploring a dataset with Bio.PopGen, How to do it…, There's more...
  • Bioconductor
    • URL / How to do it…, There's more…, See also
  • Biopython
    • URL / See also, See also, See also
    • SeqIO page, URL / See also, How to do it…
    • coalescent, simulating with / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, There's more..., See also
    • about / Introduction
    • used, for parsing mmCIF files / Parsing mmCIF files using Biopython, How to do it...
  • Biopython tutorial
    • URL / See also
  • biostars
    • URL / See also, See also
  • boot2docker
    • URL / Getting ready
  • BWA
    • URL / See also
  • bzip2
    • URL / Getting ready

C

  • CDSs
    • URL / See also
  • centromeres
    • URL / How to do it...
  • Cholroquine Resistance Transporter (CRT) / How to do it…
  • coalescent
    • simulating, with Biopython / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
    • simulating, with fastsimcoal / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
  • code
    • optimizing, Cython used / Optimizing code with Cython and Numba, How to do it..., There's more...
    • optimizing, Numba used / Optimizing code with Cython and Numba, How to do it..., There's more...
  • Coding Sequence (CDS) / How to do it…
  • comprehensions
    • reference link / There's more...
  • Copy Number Variation (CNVs) / Introduction
  • CRAN
    • URL / There's more…
  • Cython
    • used, for optimizing code / Optimizing code with Cython and Numba, How to do it..., There's more...
  • Cytoscape
    • used, for plotting protein interactions / Plotting protein interactions with Cytoscape the hard way, How to do it...
    • URL / Plotting protein interactions with Cytoscape the hard way

D

  • dataset
    • exploring, with Bio.PopGen / Exploring a dataset with Bio.PopGen, How to do it…, There's more...
  • datasets
    • managing, with PLINK / Managing datasets with PLINK, Getting ready, How to do it…, There's more...
  • Datasets.ipynb
    • URL / Getting ready
  • DAVID
    • URL / See also
  • decorators
    • URL / How to do it...
  • demographic
    • complex demographic scenarios, modeling / Modeling complex demographic scenarios, Getting ready, How to do it…
  • DendroPy
    • about / Introduction
  • Docker
    • URL / Introduction, Getting ready
    • used, for installing software / Installing the required software with Docker, How to do it…, See also

E

  • Ebola dataset
    • preparing / Preparing the Ebola dataset, How to do it..., There's more...
    • references / See also
  • Ebolavirus
    • about / Getting ready
    • reference link / Getting ready
  • EIGENSOFT
    • URL / Getting ready
  • Ensembl
    • URL / There's more…, See also, See also
    • gene ontology information, retrieving / Retrieving gene ontology information from Ensembl, How to do it..., There's more...
  • Ensembl REST API
    • used, for finding orthologues / Finding orthologues with the Ensembl REST API, How to do it..., There's more...
    • URL / There's more...
  • ETE
    • about / There's more...
    • URL / There's more...
  • executor
    • URL / There's more...
  • exons
    • URL / See also
  • extensions
    • URL / See also
    • third-party magic extensions, URL / See also

F

  • F-statistics
    • computing / Computing F-statistics, How to do it…
    • URL / See also
  • FASTQ format
    • URL / See also
  • fastsimcoal
    • coalescent, simulating with / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, There's more..., See also
    • URL / Getting ready, See also
  • fastStructure
    • URL / Investigating population structure with Admixture
  • First-In First-Out (FIFO)
    • about / How to do it...
  • Flybase
    • URL / See also
  • forward-time simulations
    • about / Introducing forward-time simulations, How to do it..., There's more...
  • FST (Fixation index) / Introduction

G

  • GATK
    • URL / See also
  • GATK annotated file
    • URL / Getting ready
  • GBIF
    • about / Introduction
    • URL / Accessing the Global Biodiversity Information Facility
    • accessing / Accessing the Global Biodiversity Information Facility, How to do it..., There's more...
    • REST API, URL / There's more...
    • datasets, geo-referencing / Geo-referencing GBIF datasets, How to do it..., There's more...
    • REST interface, URL / There's more...
  • GenBank
    • accessing / Accessing GenBank and moving around NCBI databases, How to do it…, There's more…
  • GeneAlEx
    • URL / See also
  • gene ontology
    • information, retrieving from Ensembl / Retrieving gene ontology information from Ensembl, How to do it..., There's more...
    • URL / There's more..., See also
  • Gene Ontology (GO)
    • about / How to do it...
  • Genepop
    • URL / Introduction, Getting ready, Getting ready
  • Genepop format
    • about / Introducing the Genepop format, How to do it…
    • URL / See also
  • generators
    • about / Thinking with generators, How to do it...
    • expressions, URL / See also
  • genes
    • extracting from reference, annotations used / Extracting genes from a reference using annotations, How to do it…, There's more..., See also
  • genetic data
    • aligning / Aligning genetic and genomic data, Getting ready, How to do it...
  • genome
    • accessibility / Studying genome accessibility and filtering SNP data, How to do it…, There's more…, See also
  • genomes
    • 1000 genomes project, URL / Interfacing with R via rpy2, See also
    • high-quality reference genomes / Working with high-quality reference genomes, Getting ready, How to do it..., There's more...
    • reference genomes, URL / See also
    • URL / See also, There's more...
    • annotations, traversing / Traversing genome annotations, How to do it..., There's more...
    • browser, URL / There's more...
  • genomic data
    • aligning / Aligning genetic and genomic data, Getting ready, How to do it...
  • genomics
    • data results FAQ, URL / See also
  • geometric operations
    • performing / Performing geometric operations, How to do it..., There's more...
  • Gephi
    • URL / There's more...
  • GFF spec
    • URL / See also
  • gffutils
    • URL / There's more...
  • ggplot
    • URL / There's more…
  • Git
    • URL / Getting ready, Getting ready, Getting ready
  • Global Interpreter Lock (GIL)
    • URL / There's more...
  • graph drawing
    • reference link / There's more...
  • graphviz
    • URL / See also, Getting ready
    • about / Getting ready
  • grep tool
    • about / How to do it...
  • GTF
    • URL / See also

H

  • HapMap
    • URL / Getting ready
  • hydrogen detection
    • reference link / There's more...

I

  • Illumina
    • URL / See also
  • IPython
    • used, for performing R magic / Performing R magic with IPython, How to do it…
    • used, for performing parallel computing / Performing parallel computing with IPython, How to do it...
    • parallel architecture, URL / Getting ready
    • parallel functionality, URL / There's more...
  • IPython magics
    • URL / See also
  • IPython Notebook
    • URL / See also
  • itertools
    • URL / How to do it...
  • IUPAC ambiguity codes
    • URL / See also

K

  • KEGG
    • URL / There's more...

L

  • lambda function
    • reference link / There's more...
  • Last-In First-Out (LIFO)
    • about / How to do it...
  • lazyness
    • programming with / Programming with laziness, How to do it..., There's more...
  • Linkage Disequilibrium
    • URL / See also

M

  • MAFFT
    • about / Aligning genetic and genomic data
    • URL / Aligning genetic and genomic data
  • Map Services
    • URL / Geo-referencing GBIF datasets
  • median
    • in large dataset, approximating / Computing the median in a large dataset, How to do it..., There's more...
  • minimum allele frequency (MAF)
    • about / Setting the stage for high-performance computing
  • mitochondrial matrix
    • URL / There's more...
  • mmCIF files
    • parsing, Biopython used / Parsing mmCIF files using Biopython, How to do it...
  • mmCIF format
    • URL / There's more...
  • molecular-interaction databases
    • accessing, with PSIQUIC / Accessing molecular-interaction databases with PSIQUIC, How to do it...
  • molecular distances
    • computing, on PDB file / Computing molecular distances on a PDB file, How to do it...
  • multiple databases
    • protein, finding / Finding a protein in multiple databases, How to do it..., There's more...
  • MUSCLE
    • URL / Aligning genetic and genomic data
    • about / Aligning genetic and genomic data
  • MySQL tables
    • URL / See also

N

  • NCBI
    • about / Accessing GenBank and moving around NCBI databases
    • URL / Getting ready
    • data, searching / How to do it…, There's more…
    • data, fetching / How to do it…, There's more…
    • databases, URL / See also
  • NetworkX graph processing library
    • URL / Plotting protein interactions with Cytoscape the hard way
  • NGS
    • URL / See also
    • about / Introduction
  • notebook
    • URL / Getting ready
  • Numba
    • used, for optimizing code / Optimizing code with Cython and Numba, How to do it..., There's more...
    • URL / There's more...

O

  • OpenStreetMap
    • URL / Geo-referencing GBIF datasets, There's more...
  • orthologues
    • finding, Emsembl REST API used / Finding orthologues with the Ensembl REST API, How to do it..., There's more...

P

  • P. falciparum genome
    • URL / Getting ready
  • Panther
    • URL / See also
  • parallel computing
    • performing, with IPython / Performing parallel computing with IPython, How to do it..., There's more...
  • PCA
    • about / Performing Principal Components Analysis, How to do it…
    • URL / See also
  • PDB file
    • information, extracting / Extracting more information from a PDB file, How to do it...
    • molecular distances, computing / Computing molecular distances on a PDB file, How to do it...
  • PDB file format
    • reference link / Getting ready
  • PDB parser
    • implementing / Implementing a basic PDB parser, How to do it..., There's more...
  • Phred quality score
    • URL / How to do it…, See also
  • phylogenetics
    • about / Introduction
  • phylogenetic trees
    • reconstructing / Reconstructing phylogenetic trees, Getting ready, How to do it..., There's more...
    • rooted trees / Playing recursively with trees
    • unrooted trees / Playing recursively with trees
    • visualizing / Visualizing phylogenetic data, How to do it..., There's more...
  • Picard
    • URL / See also
  • Pillow
    • URL / Geo-referencing GBIF datasets
  • PlasmoDB
    • URL / See also
  • PLINK
    • URL / Introduction, How to do it…, See also, How to do it…, Getting ready
    • datasets, managing with / Managing datasets with PLINK, Getting ready, How to do it…, There's more..., See also
  • poor human concurrent executor
    • designing / Designing a poor human concurrent executor, How to do it..., There's more...
  • population structure
    • investigating, with admixture / Investigating population structure with Admixture, How to do it…, There's more...
    • URL / Investigating population structure with Admixture
    • simulating, island model used / Simulating population structure using island and stepping-stone models, How to do it…
    • simulating, stepping-stone model used / Simulating population structure using island and stepping-stone models, How to do it…
  • Project Jupyter / Getting ready
  • protein
    • finding, in multiple databases / Finding a protein in multiple databases, How to do it..., There's more...
  • Protein Data Bank
    • about / Introduction
  • protein interactions
    • plotting, Cytoscape used / Plotting protein interactions with Cytoscape the hard way, How to do it..., There's more...
  • proteomics
    • about / Introduction
  • PSI-MI TAB 2.7 format
    • URL / How to do it...
  • PSIQUIC
    • URL / Accessing molecular-interaction databases with PSIQUIC
    • used, for accessing molecular-interaction databases / Accessing molecular-interaction databases with PSIQUIC, How to do it...
  • pygenomics
    • URL / Getting ready, Getting ready, Getting ready, How to do it…
  • pygraphviz
    • URL / Getting ready
    • about / Getting ready
  • PyMol
    • used, for animation / Animating with PyMol, How to do it..., There's more...
    • URL / Getting ready, There's more...
  • PyProt
    • URL / There's more...
  • Python distribution
    • URL / See also
  • Python library
    • URL / There's more...
  • Python software
    • list / Getting ready

R

  • R
    • URL / How to do it…, See also, See also
    • interfacing with, rpy2 used / Interfacing with R via rpy2, How to do it…, There's more…
    • magic, performing with IPython / Performing R magic with IPython
  • RAxML
    • about / Getting ready
    • URL / Getting ready
  • recursive programming
    • with trees / Playing recursively with trees, How to do it...
  • reference
    • genes extracting from, annotations used / Extracting genes from a reference using annotations, How to do it…, There's more..., See also
  • references
    • low-quality reference genomes / Dealing with low-quality genome references, Getting ready, How to do it..., There's more...
  • RepeatMasker
    • URL / See also
  • rpy2
    • used, for interfacing with R / Interfacing with R via rpy2, How to do it…, There's more…
  • rpy library documentation
    • URL / See also

S

  • SAM/BAM format
    • URL / See also
  • seaborn
    • URL / Getting ready
  • selection
    • simulating / Simulating selection, How to do it…
  • SEQanswers
    • URL / See also
  • Sequence Alignment/Map (SAM) format
    • URL / Working with alignment data
  • sequence analysis
    • performing / Performing basic sequence analysis, How to do it…, There's more…
  • sequence formats
    • working with / Working with modern sequence formats, Getting ready, How to do it…, There's more…, See also
  • simcoal
    • URL / See also
  • simulation
    • forward-time simulations / Introducing forward-time simulations, How to do it..., There's more...
    • selection / Simulating selection, How to do it…, There's more...
    • population structure, island model used / Simulating population structure using island and stepping-stone models, How to do it…
    • population structure, stepping-stone model used / Simulating population structure using island and stepping-stone models, How to do it…
    • coalescent, with fastsimcoal / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
    • coalescent, with Biopython / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
  • simuPOP
    • about / Getting ready
    • URL / There's more...
  • Single-nucleotide Polymorphisms (SNPs) / There's more…
  • smartpca
    • URL / See also
  • SNP data
    • filtering / Studying genome accessibility and filtering SNP data, Getting ready, How to do it…
  • SnpEff
    • URL / Getting ready
  • stage
    • setting, for high-performance computing / Setting the stage for high-performance computing, How to do it...
  • Structural Bioinformatics FAQ
    • URL / Getting ready

T

  • tiling coordinates
    • URL / There's more...
  • TP53 protein
    • reference link / Introducing Bio.PDB
  • trees
    • recursive programming / Playing recursively with trees, How to do it...
    • reference link / There's more...
  • TrimAl
    • about / Getting ready
    • URL / Getting ready

U

  • UCSC Genome Bioinformatics
    • URL / There's more…
  • UCSC genome browser
    • URL / See also
  • UniProt's REST interface
    • URL / There's more...

V

  • VCF
    • data, analyzing / Getting ready, How to do it…
    • URL / See also
  • VectorBase
    • URL / See also
  • virtualenv
    • URL / There's more…

W

  • well-known text
    • URL / There's more...
  • Whole Genome Sequencing (WGS) / Introduction

X

  • Xcode
    • URL / Getting ready