The recommended reading for lectures 9 and 10 is sections 6.6 and 6.7 of the book. Note that we will cover two topics (general gap penalties and affine gap penalties) that are not in the K&T book. If you want to read a resource on this topic apart from the slides, it is covered in section 1.7 of “Handbook of Computational Molecular Biology” (Aluru), which can be views via e.g. Google Books.

The recommended reading for this lecture is 6.1, 6.2 and 6.4 of the book.

The recommended reading for lecture 7 is 5.5 of the book and the Linear work suffix array construction paper. There is also a nice blog post on DC3 for those wanting another exposition as well.