Schedule, Fundamentals of Sequence Analysis, 1995-1996

Location:      158 Braun
Meeting time:  Thursdays, 12:00 - 13:00
               Yes, you may eat lunch in class

Topics to be covered:

Jan. 11   Organization
          Computing fundamentals:
            Accounts, logging in, charges
            Using the operating system utilities
            Using the GCG software

Jan. 18   Sequence alignment fundamentals
            Distance
            Gaps (indels)
            Mismatch penalties
            Dot matrices
            Aligning two sequences
            Aligning multiple sequences
            Aligning small conserved regions in multiple sequences
            Substitution Matrices
          
Jan. 25   Databases
            Names, locations, and contents
            Submitting, correcting, and retrieving entries
            Searching sequence databases:
                Finding entries homologous to a query sequence
                Finding entries containing a query pattern
                Finding entries with specific documented properties
            Searching a sequence with a pattern database

Feb.  1   Tools for Molecular Biology I, DNA:
              Mapping
              Finding genes or coding regions
              Making primers
              Engineering translationally silent restriction sites

Feb.  8   Tools for Molecular Biology II, more DNA:
              Assembling sequences

Feb. 15   Tools for Molecular Biology III, Protein:
              Mapping
              Reverse Translation
              Calculating and displaying properties
              Identifying proteins from digests

Feb. 22    Phylogenetic Analysis
              
Feb. 29    Formatting Data for publication
              Sequences
              Restriction Maps
              Multiple aligned sequences
              Output options
             
Virtual lectures (only on the Web site)
1           RNA folding