1. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Chapter 8 Genomic Analysis © 2012 John Wiley & Sons, Ltd.

2. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.1 Genome sequencing strategies.

3. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.2 Pyrosequencing.

4. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.3 Automated pyrosequencing.

5. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.4 Principle of SOLiD sequencing. (Continued)

6. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.4 (Continued).

7. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.5 Principle of Solexa/Illumina sequencing.

8. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.6 Repetitive elements cause a problem in sequencing.

9. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.7 Open reading frames: computer mapping of stop codons. Edited display from an analysis of a DNA sequence using Artemis.

10. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.8 Introns and exons.

11. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.9 Sequence annotation (EMBL) of a genomic clone. Some elements of the annotation have been omitted, and sequence data are truncated.

12. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.10 Open reading frames: display of coding sequences. Edited display from analysis of a DNA sequence and databank annotations, using Artemis.

13. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.11 Variation in genomic G+C content. The figure shows edited Artemis output displaying part of the genome sequence of E. coli. The upper part shows the base composition (G+C%) and the lower part shows the genes identified in each reading frame.

14. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.12 Inverted and direct repeats.

15. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.13 Formation of a stem-loop structure.

16. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.14 DNA-binding of regulatory proteins: nuclear receptor family.

17. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.15 Genome sequence comparisons using ACT. (a) Comparison of the genome sequences of Shigella sonnei (top) and E. coli (bottom). (b) Detailed comparison of a shorter region of the same sequences.

18. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.16 Genome structure comparison using gMAP.

19. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.17 Chromosome walking.

20. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.18 Transposon mutagenesis.

21. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.19 Locating an integrated transposon by inverse PCR.

22. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.20 Transposition of P elements in Drosophila.

23. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.21 Signature-tagged mutagenesis.

24. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.22 In vivo expression technology (IVET).

25. From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd. Figure 8.23 RNA interference.