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)   
                        Intro to alignment lecture   (Josh Korn)
                        Global alignment lecture (Saghan Madbhari)
                Local alignment    PDF
                        Local alignment lecture (Ankita Tanwar)

                Affine gap penalty     PDF          
                        Affine gap lecture (Aditi Thuse)    

                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)

    - Additional reading: Handbook of computational molecular biology - Chapter 1

Exact Matching

    - Introduction to look-up tables and BLAST PPT PDF
                    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

    - Additional reading: Durbin et al. - Chapters 1-4

Proteomics    PDF

Genome scale problems

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


    - Additional reading: Gusfield - Chapter 17




    - Here is a good position paper by Sean Eddy about the general direction of computational biology & bioinformatics.

    - A list of course-relevant journals in the area of bioinformatics and computational biology:


            BMC Bioinformatics

            Genome Research

            IEEE/ACM Transactions on Computational Biology and Bioinformatics

            Journal of Computational Biology

            Nucleic Acids Research

            PLoS Computational Biology