Cpt S 471/571:    LECTURE NOTES

PDF links to lecture notes will be updated as the course progresses.

Course introduction PDF PPT

Introduction to computational biology and bioinformatics PDF  PPT

Sequence alignments

- dynamic programming and alignment models:

Alignment introduction and global alignment    PDF    (example alignment PPT)
Scribes:
Intro to alignment lecture   (Josh Korn)

Local alignment    PDF
Scribes:
Local alignment lecture (Ankita Tanwar)

Affine gap penalty     PDF
Scribes:

Semi-global    PDF
Scribe:         Semi-global lecture

- space-optimal global alignment    PDF

Scribe:         space optimal alignment (Hao Yuan)

- K-band algorithm    PDF

Scribes Part 1 Part 2   (Z. Wang, Md. R. Islam)

- Edit distance, other distance measures  PDF

Scribe: Edit Distance (Md. Omar)

Exact Matching

- Introduction to look-up tables and BLAST
Scribe: Exact Matching intro (D. Jinguji)

- Look-up table construction and introduction to TRIES (tries, compacted tries and PATRICIA trees)    PDF
Scribe: Lookup Table and Tries (Lei Cai)

- Suffix trees PDF
Scribe: Suffix trees definition (Reza Rahman Chaudhury)

- Suffix tree basic applications: Pattern matching, longest common substring  PDF

Scribe: Suffix trees basic applications (Reza Rahman Chaudhury, Hongyang Cao)

- Linear time construction algorithm (McCreight's algo)    PDF
Detailed algorithmic pseudocode: PDF
Here is an example for simulating McCreight algorithm PPT PDF

Scribe:         McCreight's algorithm part 1  (Josh Korn)
Scribe:         McCreight's algorithm part 2  (Trevor Larson)
Scribe:         McCreight's algorithm part 3  (Aditi Thuse)

- Bender-Farach algorithm for finding the Longest Common Ancestor (LCA) in a suffix tree   PDF
Scribe:        LCA algorithm part 1 (Saghan Madbhari)
Scribe:        LCA algorithm part 2 (Hao Yuan)
Scribe:        LCA algorithm part 3 (Zhengyang Wang)

- Suffix tree advanced applications: approximate matching, restriction enzyme site, RNAi elements, suffix-prefix matching, maximal matching    PDF

- Suffix array and LCP array, space efficiency    PDF
Scribe:         Suffix array and LCP array part 1  (Aditi Thuse)
Scribe:        Suffix array (part 2)

- Burrows Wheeler Transform (BWT)  PDF

- Additional reading: Handbook of computational molecular biology - Chapters 5, 6

Probabilistic modeling for biological sequence analysis

- Probabilistic modeling PDF

- Markov chains and Hidden Markov Models    PDF

- Viterbi decoding, Forward and Backward algorithms, and their use-cases    PDF

- HMM-based sequence alignment    PDF

Proteomics    PDF

Genome scale problems

- Additional reading: Handbook of computational molecular biology - Chapters 8,9, 13

Phylogenetics