Getting Started in Molecular Information Theory
and the Delila System

This is a 'course' in what to read in molecular information theory and the Delila system to get started towards making your own sequence logos and sequence walkers. Be sure to look at the links on the main page too!

Theory

• Read the primer: Information Theory Primer to get started with information theory.
• Learn how we measure the information in binding sites: Information Content of Binding Sites
• Then you are ready to read about how logos work: A New Way to Display Consensus Sequences
• Then you are ready to see why consensus sequences are poor models: Consensus Sequence Zen
• Given that logos show an average picture, how do we look at individual binding sites? This is the individual information, read: Information Content of Individual Genetic Sequences
• Like logos, we want to be able to see the individual binding sites. For that we have sequence walkers: Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences
• For projects involving multi-part binding sites: Anatomy of Escherichia coli Ribosome Binding Sites and Anatomy of Escherichia coli sigma⁷⁰ promoters
• You can use the glossary to look up terms: A Glossary for Molecular Information Theory and the Delila System

Practice

• Unix commands.
• The Delila system of programs and tools is what you'll use. A starting point: Delila: Software for Information Analysis of Protein and Nucleic-acid Sequences

Schneider Lab
origin: 2007 May 17
updated: 2012 Feb 09