Catalog Course Description
General Description
Course Outline
Required Texts
Known hard copy typos
Known html typos
Disclaimer
Return to VADMS Instructional Activities
Catalog Course DescriptionIntroduction to Molecular Biology Computer Techniques 1 (1-6) Prereq BC/BP 364, GenCB 301. Computer analysis of protein and nucleic acid sequence, molecular visualization and modeling, sequence and structure databases.
General DescriptionStudents are given hands on experience using the computer to work on the analysis, characterization and visualization of nucleotide and protein sequences. They run through an automated demo at the start of each week's laboratory session to get a feeling for that week's activities and then work through a series of exercises to further understand the topics to be covered.
The course is organized as follows: 2 three hour lab sessions per week plus a one hour discussion period. A problem set is due each week as well.
Each student has accounts on the VADMS computers in which they carry out their assignments. They use local resources as well as INTERNET ones to complete their tasks.
Course OutlineBC/BP 378 is primarily a laboratory course. The following is a listing of brief summaries of each week's activities with a link to the actual exercise. Those weeks with links whose description doesn't include information on the size of the document will not produce printed output that exactly matches the hard copy version of the material with the Netscape browser.
Lab Manual for weeks 1 - 5
Week 1: Introduction through
visualization of biologically important molecules. Students will work
through demos that acquaint them with viewing molecules in three
dimensions. Each demo will end with the student having to
do some simple aspect of the visualization process. [56k doc with 3 gifs]
Author: Susan Jean Johns
Week 2: Introduction and background information on computers and the UNIX platform -- the nature of the computing equipment used in the course, making connections, the UNIX environment, keyboard mapping, using the pico editor, the pine e-mail utility, and communicating with other users. [100k doc with 1 gif] Author: Susan Jean Johns
Week 3: Beginning protein sequence analysis. Protein databases, the symbols used, content and organization; protein sequence data entry and manipulation, SEQED use, format conversions; physical characteristics of proteins, proteolytic digestion, molecular weight determination, composition, isoelectric point determination; and database string searches. [82k doc with 3 gifs] Author: Susan Jean Johns
Week 4: More protein sequence analysis. Further protein characteristics, including hydrophathy, hydrophobic moment determinations, amphipathicity, and secondary structure predictions. [78k doc with 4 gifs] Author: Susan Jean Johns
Week 5: Protein visualization and manipulation. Color coding protein physical characteristics such as residue charge, hydrophobicity, and secondary structure elements, and making physical measurements. [76k doc with 4 gifs] Author: Susan Jean Johns
Lab Manual for weeks 6-9
Week 6: Beginning DNA sequence
analysis. Nucleic acid databases, the
symbols used, content and organization; DNA sequence data entry and
manipulations, SEQED use for nucleotide data, revised keyboard mapping; DNA
physical characteristics, restriction enzyme cutting sites, and
composition. [77k doc with 2 gifs] Author: Susan Jean Johns
Week 7: More DNA sequence analysis. Gene finding strategies, including open reading frame analysis; identifying functional elements, including promoters, terminators, and sequence repeats. [101k doc with 2 gifs] Author: Steven M. Thompson
Week 8: Oligonucleotide probe design and DNA fingerprinting. Starting from known polymorphic DNA sequences, you will use PCR primer design software to create a probe, test it for effectiveness, run restriction digests on the product and solve the forensics puzzle. [56k with 7 gifs] Author: Steven M. Thompson
Week 9: DNA visualization. Generate simple DNA structures, color code DNA chains, show hydrogen bonding patterns in different DNA conformations, and visualize DNA interactions with other molecules. [61k doc with 2 gifs] Author: Susan Jean Johns
Lab Manual for weeks 10 - 14
Week 10: Database similarity
searching and dynamic programming algorithms. Advantages and
disadvantages of protein versus DNA searching, Dayhoff and other
substitution matrices, dot matrix methods, pairwise alignments, hashing
algorithms, and network based database searching. [124 k doc with 3 gifs]
Author: Steven M. Thompson
Week 11: Multiple sequence alignment. Progressive, pairwise multiple sequence alignment algorithms and profile development and analysis. Also covers visualization tools for multiple sequence alignments. [160k doc with 6 gifs] Author: Steven M. Thompson
Week 12: Evolutionary studies. Homology versus similarity, the relationships of protein and DNA sequences across and within species. How to infer and represent phylogenetic trees. [156k doc with 6 gifs] Author: Steven M. Thompson and Susan Jean Johns
Week 13: Small molecule modelling using MacroModel. Entering small organic molecules and peptides into the computer, defining structure, energy minimization, and solvent effects. [67k doc with 3 gifs] Author: Susan Jean Johns
Week 14: Homology modelling. How to relate information from different types of analyses, use the NRL_3D database to find structural information, and network tools for generating structural information. [82 k doc] Author: Susan Jean Johns
Required TextsThe following textbooks are required for BC/BP 378:
Sequence Analysis Primer, Michael Gribskov and John Devereux, eds., W.H.
Freeman and Company, New York (1992), ISBN 0-7167-7002-4
new: $ 35.95 used: unknown
lab manual for weeks 1-5, ISBN 0000041254
new: $13.55
lab manual for weeks 6-9, ISBN 0000041262
new: $11.85
lab manual for weeks 10-14, ISBN
new: $19.30
Known hard copy typos The following is a listing of the typos found in the BC/BP 378 manuals sold through the Bookie for the fall 96.
Week 6:- E-mail address for the retrieve server at NCBI (on page 13).
The address should read retrieve@ncbi.nlm.nih.gov not what is
given on the page.
Known html typos The following is a listing of the typos found in the BC/BP 378 html versions of the manuals for the fall 96.
Week 5:- At the top of page 10, draw in single bonds between the two nitrogens of the histidine ring and carbon between them.
DisclaimerThe materials presented here are unique to the Washington State University campus. They require the assignments made on the VADMS computing platforms in order to work properly. They are only presented here as examples of instructional materials in biocomputing education field.
In the html versions of these materials a colored bar serves as a divider between such items as the cover page and the rest of the text, the background materials and the actual exercise, the exercise and any appendixes or other included materials. [It has been noted that not all printers produce the gif images as they were intended to be.]