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Guide to Bioinformatics with BioPython

version 1.4, revised for BioPython version 1.56

 

Chapter 1. Introduction

  • What is Biopython?
  • Installing Biopython

Chapter 2 Quick Start – What can you do with Biopython?

  • 2.1 General overview of what Biopython provides
  • 2.2 Working with sequences
  • 2.3 A usage example
  • 2.4 Parsing sequence file formats
    • 2.4.1 Simple FASTA parsing example
    • 2.4.2 Simple GenBank parsing example
  • 2.4.3 I love parsing – please don’t stop talking about it!
  • 2.5 Connecting with biological databases
  • 2.6 What to do next


Chapter 3 Sequence objects

  • 3.1 Sequences and Alphabets
  • 3.2 Sequences act like strings
  • 3.3 Slicing a sequence
  • 3.4 Turning Seq objects into strings
  • 3.5 Concatenating or adding sequences
  • 3.6 Changing case
  • 3.7 Nucleotide sequences and (reverse) complements
  • 3.8 Transcriptio
  • 3.9 Translation
  • 3.10 Translation Tables
  • 3.11 Comparing Seq objects
  • 3.12 MutableSeq object
  • 3.13 UnknownSeq objects
  • 3.14 Working with directly strings

Chapter 4 Sequence Record objects

  • 4.1 The SeqRecord object
  • 4.2 Creating a SeqRecord
    • 4.2.1 SeqRecord objects from scratch
    • 4.2.2 SeqRecord objects from FASTA files
    • 4.2.3 SeqRecord objects from GenBank files
  • 4.3 SeqFeature objects
    • 4.3.1 SeqFeatures themselves
    • 4.3.2 Locations
  • 4.4 References
  • 4.5 The format method
  • 4.6 Slicing a SeqRecord
  • 4.7 Adding SeqRecord objects

Chapter 5 Sequence Input/Output

  • 5.1 Parsing or Reading Sequences
    • 5.1.1 Reading Sequence Files
    • 5.1.2 Iterating over the records in a sequence file
    • 5.1.3 Getting a list of the records in a sequence file
    • 5.1.4 Extracting data
  • 5.2 Parsing sequences from the net
    • 5.2.1 Parsing GenBank records from the net
    • 5.2.2 Parsing SwissProt sequences from the net
  • 5.3 Sequence files as Dictionaries – In memory
    • 5.3.1 Specifying the dictionary key
    • 5.3.2 Indexing a dictionary using the SEGUID checksum
  • 5.4 Sequence files as Dictionaries – Indexed files
    • 5.4.1 Specifying the dictionary keys
    • 5.4.2 Getting the raw data for a record
    • 5.4.3 Discussion
  • 5.5 Writing Sequence Files
    • 5.5.1 Round trips
    • 5.5.2 Converting between sequence file formats
    • 5.5.3 Converting a file of sequences to their reverse complements
    • 5.5.4 Getting your SeqRecord objects as formatted strings

Chapter 6 Multiple Sequence Alignment objects

  • 6.1 Parsing or Reading Sequence Alignments
    • 6.1.1 Single Alignments
    • 6.1.2 Multiple Alignments
    • 6.1.3 Ambiguous Alignments
  • 6.2 Writing Alignments
  • 6.2.1 Converting between sequence alignment file formats
  • 6.2.2 Getting your alignment objects as formatted strings
  • 6.3 Manipulating Alignments
  • 6.4 Alignment Tools
    • 6.4.1 ClustalW
    • 6.4.2 MUSCLE
    • 6.4.3 MUSCLE using stdout
    • 6.4.4 MUSCLE using stdin and stdout
    • 6.4.5 EMBOSS needle and water

Chapter 7 BLAST

  • 7.1 Running BLAST over the Internet
  • 7.2 Running BLAST locally
  • 7.3 Parsing BLAST output
  • 7.4 The BLAST record class
  • 7.5 Deprecated BLAST parsers
    • 7.5.1 Parsing plain-text BLAST output
    • 7.5.2 Parsing a plain-text BLAST file full of BLAST runs
    • 7.5.3 Finding a bad record somewhere in a huge plain-text BLAST file
  • 7.6 Dealing with PSI-BLAST
  • 7.7 Dealing with RPS-BLAST

Chapter 8 Accessing NCBI’s Entrez databases

  • 8.1 Entrez Guidelines
  • 8.2 EInfo: Obtaining information about the Entrez databases
  • 8.3 ESearch: Searching the Entrez databases
  • 8.4 EPost: Uploading a list of identifiers
  • 8.5 ESummary: Retrieving summaries from primary IDs
  • 8.6 EFetch: Downloading full records from Entrez
  • 8.7 ELink: Searching for related items in NCBI Entrez
  • 8.8 EGQuery: Global Query - counts for search terms
  • 8.9 ESpell: Obtaining spelling suggestions
  • 8.10 Parsing huge Entrez XML files
  • 8.11 Handling errors
  • 8.12 Specialized parsers
  • 8.12.1 Parsing Medline records
  • 8.12.2 Parsing GEO records
  • 8.12.3 Parsing UniGene records
  • 8.13 Using a proxy
  • 8.14 Examples
    • 8.14.1 PubMed and Medline
    • 8.14.2 Searching, downloading, and parsing Entrez Nucleotide records
    • 8.14.3 Searching, downloading, and parsing GenBank records
    • 8.14.4 Finding the lineage of an organism
  • 8.15 Using the history and WebEnv
    • 8.15.1 Searching for and downloading sequences using the history
    • 8.15.2 Searching for and downloading abstracts using the history
    • 8.15.3 Searching for citations

Chapter 10 Going 3D: The PDB module

  • 10.1 Structure representation
    • 10.1.1 Structure
    • 10.1.2 Model
    • 10.1.3 Chain
    • 10.1.4 Residue
    • 10.1.5 Atom
  • 10.2 Disorder
    • 10.2.1 General approach
    • 10.2.2 Disordered atoms
    • 10.2.3 Disordered residues
  • 10.3 Hetero residues
    • 10.3.1 Associated problems
    • 10.3.2 Water residues
    • 10.3.3 Other hetero residues
  • 10.4 Some random usage examples
  • 10.5 Common problems in PDB files
    • 10.5.1 Examples
    • 10.5.2 Automatic correction
    • 10.5.3 Fatal errors
  • 10.6 Other features

Chapter 11 Bio.PopGen: Population genetics

  • 11.1 GenePop
  • 11.2 Coalescent simulation
    • 11.2.1 Creating scenarios
    • 11.2.2 Running SIMCOAL2
  • 11.3 Other applications
    • 11.3.1 FDist: Detecting selection and molecular adaptation
  • 11.4 Future Developments

Chapter 12 Phylogenetics with Bio.Phylo

  • 12.1 Demo: What’s in a Tree?
    • 12.1.1 Coloring branches with PhyloXML
  • 12.2 I/O functions
  • 12.3 Viewing and exporting trees
  • 12.4 Using Tree and Clade objects
    • 12.4.1 Search and traversal methods
    • 12.4.2 Information methods
    • 12.4.3 Modification methods
  • 12.5 Features of PhyloXML trees
  • 12.6 Future plans

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