Fundamentals of Sequence Analysis Course Page, 1996

Fundamentals of Sequence Analysis Course information

All information subject to change!

Problem sets

1. Jan. 11 - computing basics

2. Jan. 18 - sequence alignment

3. Jan. 25 - databases, database searching

4. Feb. 1 - Tools for Molecular Biology I, DNA

5. Feb. 8 - Tools for Molecular Biology II, Sequence assembly

6. Feb. 15 - Tools for Molecular Biology III, Protein

7. Feb. 22 - Phylogenetic analysis

8. Feb. 29 - Formatting data for publication

8. (extra) - RNA folding

Lectures

These are the notes and figures used in the lectures, for those of you who missed one or more lectures. (The program NEDIT is used in the lectures where you would probably use TYPE or TYPE/PAGE.)

Jan. 11 Computing basics

Jan. 18 Sequence Alignment Fundamentals

Figure 1. Distance Metric

Figure 2. Smith Waterman example

Jan. 25 Databases and Database searches

Feb. 1 Tools for Molecular Biology I - DNA

Figure 1. Genefinder results

Figure 2. Proscan results

Feb. 8 Tools for Molecular Biology II - DNA sequencing and assembly

Figure 1. Fragment assembly programs, Gelassemble commands

Feb. 15 Tools for Molecular Biology III - Protein

Figure 1. Comparison of secondary structure predictions

Feb. 22 Phylogenetic analysis

Figure 1. Programs for phylogenetic analysis

Figure 2. Example for Azurin

Graphic NEIGHBOR-JOINING

Graphic PROTPARS

Feb. 29 Formatting data for publication

Figure 1. Plasmidmap example

Figure 2. Multiple sequence examples

- - RNA folding

Figure 1. Plotfold examples

Manuals or other instructional material

SAF documentation - main entry point, all topics

SAF documentation - molecular biology entry point

SAF documentation - OpenVMS entry point

Shortcut to OpenVMS User's Manuals

Shortcut to Overview - OpenVMS command basics

Shortcut to OpenVMS beginners FAQ

Shortcut to GCG beginners FAQ

Relevant Web pages