Objective:  The objective of this course is to introduce students to currently available programs for computational analysis of nucleic acid and protein sequences.  Students will use programs to identify genes, compare nucleic acid and protein sequences, predict secondary and tertiary structure, and study gene evolution.  This course will emphasize computer usage but no programming experience is required.  A course in biochemistry or molecular genetics is strongly recommended. Grading will be based upon assignments and a term project focusing upon analysis of a gene family.

Course Assignments

Lecture Notes

Syllabus

Week 1:  What is bioinformatics -
               Internet basics
               Review of nucleic acids; amino acids; proteins and genes
               gene families superfamilies, motifs

Week 2: Recombinant DNA and DNA sequencing
                    Methods
                    Automated gel reading
                    Primer Design
                    Restriction Endonuclease mapping
                    Translation

Week 3    Databases:
                    Searches 
                    What does it all mean?
                    GCG program

                  Alignment programs
                       Basic principals
                       mutation matrix
                       global vs local aligment
                       repetitive elements and low complexity regions
                   Dot plots 
                   Multiple sequence alignments

Week 4     Alignment continued
                    Protein vs Nucleic Acid searches/alignments
                    Blast
                    Fasta
                    Scoring
                    Evaluation of matches
 
Week 5   Gene Structure (promoter elements, splicing, termination)
                    Gene identification methods: grail etc
                    Comparison of methods

Week 6  Protein structure/function predicition
                      Profiles construction and searches
                      Motif searching
 

Week 7 Protein Structure/function
                      Secondary Structure prediction (GOR, Chou/Fassman etc)
                      Tertiary Structure Prediction

Week 8 Protein Structure/function

Week 9  RNA Structure Prediction
                     tRNA
                     Regulatory functions

Week 10 Phylogeny

Week 11 Phylogeny

Week 12 Entire genome analysis/databases

Week 13 Term Project

Week 14 Term Project