Schedule, Fundamentals of Sequence Analysis, 1998-1999

Location:      151 Braun
Meeting time:  Thursdays, 12:00 - 13:00 through Feb. 4, 1999
               Tuesdays,  12:00 - 13:00 beginning Feb. 9, 1999
               Yes, you may eat lunch in class

Web Site:      http://seqaxp.bio.caltech.edu/

Topics to be covered:

Jan. 21   Organization
          Computing fundamentals:
            Accounts, logging in, charges
            Using the operating system utilities
            Using the GCG software

Jan. 28   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
          
Feb.  4   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.  9   Tools for Molecular Biology I, DNA:
            Mapping
            Finding genes or coding regions
            Making primers
            Engineering translationally silent restriction sites
            Cloning problems

Feb. 16   Tools for Molecular Biology II, more DNA:
            Assembling sequences

Feb. 23   Tools for Molecular Biology III, Protein:
            Mapping
            Reverse Translation
            Calculating and displaying properties
            Identifying proteins from digests

Mar.  2    Phylogenetic Analysis
              
Mar.  9    Formatting Data for publication
             Sequences
             Restriction Maps
             Multiple aligned sequences
             Output options

Mar. 16    RNA folding
Mar. 23    Survey of Web based tools
             Search/retrieve by keyword or other "comment".
             Search databases by sequence