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3. Data Structures

4. Graphs

4.2.1 Eulerian paths

Exercises

5. Network flows

5.4 Covering problems

6. Alignments

6.1.2 Shortest detour

7. Hidden Markov models (HMMs)

Insight 7.1

Exercises

8. Classical Indexes

8.3 Suffix tree

8.4 Applications of the suffix tree

8.5 Literature

9. Burrows-Wheeler indexes

9.7.1 Frequency-oblivious representation

9.7.3 Space-efficient construction

9.8 Literature

Exercises

11. Genome analysis and comparison

11.1 Space-efficient genome analysis

11.2 Comparing genomes without alignment

11.3 Literature

Exercises

13. Fragment assembly

13.5 Literature

Exercises

14. Genomics

Exercises

15. Transcriptomics

15.4 Transcript alignment with co-linear chaining


References