BC/BP 578 Course
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Return to VADMS Instructional Activities
Molecular Biology Computer Techniques 4 (2-6) Prereq BC/BP 364 or 563;
GenCB 301. Computer analysis of protein and nucleic acid sequence,
secondary structure prediction, protein folding, homology searches and
uses of databases. Cooperative course taught by WSU, open to UI students
(MMBB 578).
This course is a lecture/laboratory course with emphasis placed on
acquiring bioanalytical computing skills. Students are given hands on
experience using the computer in either a sequence analysis or
molecular modelling track and then are expected to apply their skills to
their own project of interest.
The course is organized as follows: 3 one hour lectures per
week for the first 10 weeks of the semester plus at least one three hour
lab session for the same time period. The rest of the time is dedicated
to the semester project. The time spent in lab escalates as the semester
progresses.
Each student is given the necessary account(s) on VADMS platforms in
which to carry out their assignments. They use local resources as well as
INTERNET ones to complete their tasks.
BC/BP 578 is mainly a laboratory course enhanced by lectures. 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 are not available yet.
Lab Manual for weeks 1 - 3
Week 1: A tour of the
computing resources available to you in this course. [29K doc with 1 gif]
Author: Susan Jean Johns
Week 2: A basic
introduction to the computing platforms on which this course will be
taught. Items covered include background information on computers, the
nature of the computing resources to be used, and instructions on using
the text editor. [59K doc with 1 gif] Author: Susan Jean Johns Also
included Unix for Beginners.
Week 3: Learning about the
concept of databases and how they are organized. Discovering the
databases in the VADMS system and learning how to gather
information from them. Exploring the nets for more biocomputing
databases. [59K doc] Author: Susan Jean Johns
Lab Manual for weeks 4 - 7
Week 4 - molecular modelling
Learning about entering data for various uses. Exploring data formats
and how to use them. [110K doc with 3 gifs] Author: Susan
Jean Johns
Week 4 - sequence analysis
Learning about entering data for various uses. Exploring data formats
and how to use them. [83K doc with 1 gif] Author: Susan
Jean Johns
Week 5 - molecular modelling
Learning about the ways to estimate protein secondary structures and
the usefulness of these techniques for other purposes. [49K doc with 2
gifs] Author: Susan Jean Johns
Week 5 - sequence analysis
Unknown DNA: Rational Probe Design and Analysis -- the "Guessmer." How to
design and analyze oligonucleotide probes and primers for discovering
genes in organisms where they have not been identified when the gene's
encoded protein sequence is known in other organisms. [100K doc with 3
gifs] Author: Steven M.Thompson
Week 6 - molecular modelling
Learning about advanced data entry techniques. Exposure to recognizing
and correcting data input problems. Modification of data files for
specialized needs. Modification of MacroModel minimization
output files to take into account solvent effects. [76K doc with 1 gif]
Author: Susan Jean Johns
Week 6 - sequence analysis
DNA Sequencing: The GCG Fragment Assembly Package (FAS) -- getting your
fragments into the computer and assembled into a continuous sequence.
[55K doc] Author: Steven M. thomspon
Week 7 - molecular modelling
Learning about determining the physical characteristics of molecules on
the computer. Coloring the determined secondary structure of a molecule.
Creating and using alpha carbon traces and the superpositioning of
molecules. Learning about doing measurements on molecules and docking.
[78K doc ] Author: Susan Jean Johns
Week 7 - sequence analysis Gene
Finding Strategies: After the Sequencing's Done, What Next? How are coding
sequences recognized in genomic DNA? Searching by signal versus searching
by content -- transcriptional/translational regulatory sites and
exon/intron splice sites; "nonrandomness" and codon usage -- understanding
the concepts and differentiating between the approaches. [65K doc with
5 gifs] Author: Steven M. Thompson
Lab Manual for weeks 8 - 10
Week 8 - molecular modelling
Homology Modelling: combining seqeunce analysis and molecular
modelling skills to explore the theoretical modelling of unsolved
sequences based on solved ones. [108K doc] Author: Susan Jean
Johns
Week 8 - sequence analysis
Advanced Database Similarity Searching: What's available, the methods and
the algorithms -- motifs, hashing techniques and heuristics, dot matrix
analysis, multiple sequence alignments, and profiles. [151K doc with 3
gifs] Author: Steven M. Thompson
Week 9 - molecular modelling
Learning about data visualization techniques using Molscript
, RasMol and Povscript software. Recognizing desired
structural data elements and combining them with PDB formatted data
files from different sources for use in the software. [71K doc with links
to software documentation] Author: Susan Jean Johns
Week 9 - sequence analysis
Estimating protein secondary structure and physical attributes: Learning
about various methods and the usefulness and limitations of these
predictions. [105K doc with 6 gifs] Author: Susan Jean Johns
and Steven M. Thompson
Week 10 - molecular modelling
An example of solving a modelling problem. This exercise
incorporates additional sequence analysis skills to come up with a
solution to the problem at hand. [45K doc} Author: Susan Jean
Johns
Week 10 - sequence analysis
SeqLab and Molecular Evolutionary Phylogenetic Inference: How GCG's SeqLab
Graphical User Interface (GUI) to the Wisconsin Sequence Analysis
Package can be used to develop and refine input for programs from
PAUP* (Phylogenetic Analysis Using Parsimony [and other methods] and
PHYLIP (PHYLogeny Inference Package) and how to use the available
molecular evolution inference tools to ascertain and draw phylogenetic
trees. [204K doc with 17 gifs] Author: Susan Jean Johns and
Steven M. Thompson
The following lab manuals are required for BC/BP 578:
lab manual for weeks 1 - 3
new: $x.xx
lab manual for weeks 4 - 7
new: $xx.xx
lab manual for weeks 8 - 10
new: $xx.xx
The following is a listing of the typos found in the BC/BP 578 manuals
sold through the Bookie for the spring 98. This is not a complete list.
The following is a listing of the typos found in the BC/BP 578 html
versions of the manuals for the spring 98.
The 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.]
RasMol usage has been added to a number of modelling exercises.
Povscript in used briefly. Threader2 and its Px
analyst are lightly touched on as well.