Contents
Chapter 1 Introduction
1.1 What is Biopython?
1.1.1 What can I find in the Biopython package
1.2 Installing Biopython
1.3 FAQ
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 biological file formats
2.4.1 General parser design
2.4.2 Writing your own consumer
2.4.3 Making it easier
2.4.4 FASTA files as Dictionaries
2.4.5 I love parsing – please don't stop talking about it!
2.5 Connecting with biological databases
2.6 What to do next
Chapter 3 Cookbook – Cool things to do with it
3.1 BLAST
3.1.1 Running BLAST over the Internet
3.1.2 Parsing the output from the WWW version of BLAST
3.1.3 The BLAST record class
3.1.4 Running BLAST locally
3.1.5 Parsing BLAST output from local BLAST
3.1.6 Parsing a file full of BLAST runs
3.1.7 Finding a bad record somewhere in a huge file
3.1.8 Dealing with PSIBlast
3.2 SWISS-PROT
3.2.1 Retrieving a SWISS-PROT record
3.3 PubMed
3.3.1 Sending a query to PubMed
3.3.2 Retrieving a PubMed record
3.4 GenBank
3.4.1 Retrieving GenBank entries from NCBI
3.4.2 Parsing GenBank records
3.4.3 Making your very own GenBank database
3.5 Dealing with alignments
3.5.1 Clustalw
3.5.2 Calculating summary information
3.5.3 Calculating a quick consensus sequence
3.5.4 Position Specific Score Matrices
3.5.5 Information Content
3.5.6 Translating between Alignment formats
3.6 Substitution Matrices
3.6.1 Using common substitution matrices
3.6.2 Creating your own substitution matrix from an alignment
3.7 More Advanced Sequence Classes – Sequence IDs and Features
3.7.1 Sequence ids and Descriptions – dealing with SeqRecords
3.7.2 Features and Annotations – SeqFeatures
3.8 BioRegistry – automatically finding sequence sources
3.8.1 Finding resources using a configuration file
3.8.2 Finding resources through a biopython specific interface
3.9 BioSQL – storing sequences in a relational database
3.10 BioCorba
3.11 Going 3D: The PDB module
3.11.1 Structure representation
3.11.2 Disorder
3.11.3 Hetero residues
3.11.4 Some random usage examples
3.11.5 Common problems in PDB files
3.11.6 Other features
3.12 Miscellaneous
3.12.1 Translating a DNA sequence to Protein
Chapter 4 Advanced
4.1 Sequence Class
4.2 Regression Testing Framework
4.2.1 Writing a Regression Test
4.3 Parser Design
4.3.1 Design Overview
4.3.2 Events
4.3.3 'noevent' EVENT
4.3.4 Scanners
4.3.5 Consumers
4.3.6 BLAST
4.3.7 Enzyme
4.3.8 Fasta
4.3.9 Medline
4.3.10 Prosite
4.3.11 SWISS-PROT
4.4 Substitution Matrices
4.4.1 SubsMat
4.4.2 FreqTable
Chapter 5 Where to go from here – contributing to Biopython
5.1 Maintaining a distribution for a platform
5.2 Bug Reports + Feature Requests
5.3 Contributing Code
Chapter 6 Appendix: Useful stuff about Python
6.1 What the heck in a handle?
6.1.1 Creating a handle from a string