Biopython Tutorial and Cookbook

Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock

Last Update--16 March 2007

• Table of Contents
• Introduction
  • What is Biopython?
  • Installing Biopython
  • FAQ
• Quick Start -- What can you do with Biopython?
  • General overview of what Biopython provides
  • Working with sequences
  • A usage example
  • Parsing sequence file formats
  • Connecting with biological databases
  • What to do next
• Sequence objects
  • Sequences and Alphabets
  • Sequences act like strings
  • Slicing a sequence
  • Turning Seq objects into strings
  • Nucleotide sequences and (reverse) complements
  • Concatenating or adding sequences
  • MutableSeq objects
  • Transcribing and Translation
  • Working with directly strings
• Sequence Input/Output
  • Parsing or Reading Sequences
  • Parsing sequences from the net
  • Sequence files as Dictionaries
  • Writing Sequence Files
• BLAST
  • Running BLAST locally
  • Running BLAST over the Internet
  • Saving BLAST output
  • Parsing BLAST output
  • The BLAST record class
  • Deprecated BLAST parsers
  • Dealing with PSIBlast
• Bio.Entrez: Accessing NCBI's Entrez databases
  • EInfo: Obtaining information about the Entrez databases
  • ESearch: Searching the Entrez databases
  • EPost
  • ESummary: Retrieving summaries from primary IDs
  • EFetch: Downloading full records from Entrez
  • ELink
  • EGQuery: Obtaining counts for search terms
  • ESpell: Obtaining spelling suggestions
  • Creating web links to the Entrez databases
• Swiss-Prot, Prosite, Prodoc, and ExPASy
  • Bio.SwissProt: Parsing Swiss-Prot records
  • Bio.Prosite: Parsing Prosite records
  • Bio.Prosite.Prodoc: Parsing Prodoc records
  • Bio.ExPASy: Accessing the ExPASy server
• Cookbook -- Cool things to do with it
  • PubMed
  • GenBank
  • Dealing with alignments
  • Substitution Matrices
  • BioRegistry -- automatically finding sequence sources
  • BioSQL -- storing sequences in a relational database
  • BioCorba
  • Going 3D: The PDB module
  • Bio.PopGen: Population genetics
  • InterPro
• Advanced
  • The SeqRecord and SeqFeature classes
  • Regression Testing Framework
  • Parser Design
  • Substitution Matrices
• Where to go from here -- contributing to Biopython
  • Maintaining a distribution for a platform
  • Bug Reports + Feature Requests
  • Contributing Code
• Appendix: Useful stuff about Python
  • What the heck is a handle?

This document was translated from L^AT_EX by H^EV^EA and H^AC^HA.