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