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)
                        Global alignment lecture (Saghan Madbhari)
 
                Local alignment    PDF
                Scribes:
                        Local alignment lecture (Ankita Tanwar)

                Affine gap penalty     PDF          
                Scribes:
                        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

Phylogenetics

    - Additional reading: Gusfield - Chapter 17

 

 

GENERAL READING AND REFERENCES

    - 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:

            Bioinformatics

            BMC Bioinformatics

            Genome Research

            IEEE/ACM Transactions on Computational Biology and Bioinformatics

            Journal of Computational Biology

            Nucleic Acids Research

            PLoS Computational Biology