1. Pairwise and NGS read alignment

2. Sequencing again

3. Proteins first!
1951 F Sanger

4. Then come the nucleic acids
DNA battle
RNA battle

5. Alignment applications
Detect genetic determinants
Similarity in genomes
Find ortholog genes
And whatnot

6. Alignment algorithm A G C A C T

7. Alignment algorithm A G C A C T A C T G

8. Alignment algorithm A G C A C T A C T G - A C T

9. Alignment algorithm A G C A C T A C T -1 G - A C T

10. Alignment algorithm A G C A C T A C T -1 -2 G - A C T

11. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 G - A C-1 -2 -3 -4 -5 -6 -7 -8 G - A C T

12. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 G - A G-1 -2 -3 -4 -5 -6 -7 -8 G - A G C

13. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 G

14. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 G - A

15. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 G A -

16. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 1 G - A

17. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3-1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3 4 5 A C - T G

18. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3-1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3 4 5

19. Alignment algorithm A G C A C T A C T -1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3-1 -2 -3 -4 -5 -6 -7 -8 1 G 2 3 4 5 A C - T G

20. End of part one

21. What about NGS alignment?
Short reads(billions)
Genome

22. Indexing the genome

23. Burrows-Wheeler transform FM index
Last to first mapping $ a c g 1 4 6

24. Burrows-Wheeler transform EXACTMATCH
Finding the “aac” $ a c g 1 4 6

25. Burrows-Wheeler transform UNPERMUTE$ a c g 1 4 6

26. Bowtie Remember the quality! Mutations Sequencing errors G A C T
@cluster_2:UMI_ATTCCG
TTTCCGGGGCACATAATCTTCAGCCGGGCGC +
Poor quality

27. Paired-end reads

28. Paired-end read advantages
Reducing multimaps

29. Paired-end read advantages
Detection of structural variations

30. RNA-seq read mapping

31. Tophat

32. Detecting exons

33. Mapping over junctions
IUM are indexed