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Tools available to perform motif analysis
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Classroom Contents
Introduction to Motif Discovery and Transcription Factor Binding Site Analysis
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- 1 Intro
- 2 What are motifs?
- 3 What are Transcription Factors?
- 4 Structure of a gene and regulatory regions
- 5 Why is there a need for gene regulation?
- 6 Different ways to represent Motifs or Transcription Factor Binding Sites
- 7 When to perform a Transcription Factor Binding Site Analysis?
- 8 Tools available to perform motif analysis
- 9 Motif databases
- 10 Case study for demonstration using Homer
- 11 Fetch data from NCBI GEO
- 12 About Homer and notes on installation
- 13 Following Homer instructions to find motifs in genomic regions
- 14 Manipulate peak file to get it into the acceptable format
- 15 Run Homer script to find motifs
- 16 Looking at resulting files
- 17 Understanding Homer’s de novo motif finding results
- 18 Understanding Homer’s known motif canonical finding results
- 19 Find which peaks do a specific motif bind to?
- 20 Method 1 to find motif instances
- 21 Method 2 to find motif instances
