'97 BC/BP 378 Course
This area is currently under revison with this year's materials slowly
being added. The exercise section is now complete.
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Return to VADMS Instructional Activities
Introduction 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.
Students 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.
BC/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.
NOTE:-Since this course was last taught, the decision has been made
to no longer use MacroModel software. Therefore, those exercises
that use this software (weeks 5, 9, 12 and 14) have major sections in them
that will have to be re-written for use with some other visualization or
modelling tool.
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. The week's exercise will end with a RasMol movie script
of a DNA - protein structure. [ 62k 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. The WEB is explored
through VADMS own home page. [104k 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. [84k 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. [86k doc with 5 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. [81k 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. [76.5k doc with 2 gifs]
Author: Susan Jean Johns
Week 7: 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. [ 58k doc with 7 gifs] Author: Steven M.
Thompson
Week 8: More DNA sequence
analysis. Gene finding strategies, including open reading frame analysis;
identifying functional elements, including promoters, terminators, and
sequence repeats. [ 114k doc with 4 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. [64k 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. [ 135k 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. [332k doc with 9 gifs] Author:
Steven M. Thompson
Week 12: Small molecule
modelling using MacroModel. Entering small organic molecules and peptides
into the computer, defining structure, energy minimization, and solvent
effects. [79k doc with 3 gifs] Author: Susan Jean Johns
Week 13: Evolutionary studies.
Homology versus similarity, the relationships of protein and DNA sequences
across and within species. How to infer and represent phylogenetic
trees. [ 152k doc with 6 gifs] Author: Steven M. Thompson and 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. [69k doc] Author: Susan Jean Johns
The 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
This year the Bookie decided to shrink wrap all the manuals together in a
bundel that costs $ 46.20. If they could be purchased separatley the
prices would be.
lab manual for weeks 1-5
new: $14.70
lab manual for weeks 6-9
new: $11.95
lab manual for weeks 10-14
new: $19.55
The following is a listing of the typos found in the BC/BP 378 manuals
sold through the Bookie for the fall 97.
Week 1:- Towards the middle of page 9, 3'-5'' should read
3'-5'.
Week 2:- Towards the top of page 20. In order to have all the
necessary files for the rest of the exercise, add the following command
line after the practice file copy line.
% cp $UGRAD_DIR/week2/snake.seq .
% cp $UGRAD_DIR/week2/pdbtxt.txt .
% cp $UGRAD_DIR/week2/week2.week2 .
Mid section of page 23, the second copy of the following
sentence needs to be deleted. "The following functions are available in
pico (where applicable, corresponding function keys are in
parentheses)."
Week5:- At the middle of page 16, replace the phrase "skipping step
1" with "skipping steps 1 and 2".
At the top of page 21 replace FRes with NRes.
At the bottom of page 24, replace "Click three times" with Click
twice.
Week 6:- Near the top of page 14, replace the I with a
| symbol.
Near the bottom of page 15, replace % cd data_entry with % cd
dna_entry.
Near the top of page 26, replace (your lastname).image6 with
(your lastname).clone2.
Week 7:- Near the bottom of page 4, delete the following section
from the manual as it is no longer needed.
At the conclusion of the demo go to the Versa Term-Pro "Emulation"
menu and manually switch back to "DEC VT220" terminal emulation
mode.
Towards the bottom of page 15, delete the phrase for extra credit
work from the last sentence in the first paragraph on DNA
fingerprinting analysis.
Week 8:- Towards the bottom of page 11, change the first part of
the line in the second paragraph in section 4.b.3. dealing with
doing a poly(A) search to read.
Run the poly(A) search mentioned above on your chosen LD78 sequence;
At the end of the paragraph below the graphic on page 14, change
priniting to printing.
On page 24 in the conclusions and evaluations section, replace the
week7 terms with week8.
Week 9:- At the end of the last paragraph on page 3, update the
folloing numbers. 5000 should be 6000 and 300 should be
700.
On page 12 after step 12, add the following to the paragraph prior to the
one about exiting the emulator.
exercise, skipping the next paragraph and reading down to step 2 of
section a of the next part of the exercise.
Week 10:- On page 6 add the following words to the last sentence in
the second to the last paragraph.
1990) and FASTA (Pearson and Lipman, 1988) and change uses to
use.
On page 8, section 4.a.1 TFastA, add the following words to the second
sentence of the paragraph.
onsite, excluding FrameAlign/Search.
On page 39, section 5.a.2 in the fifth sentence of that paragraph change
mean to means.
Week 11:- On page 6 delete the sentence after the % demo11
line at the bottom of the page. This is not needed any more.
On page 22 under the graphics, change the words in the second sentence
from to "File" to "Printer".
On page 25 at the end of the first paragraph, change "Batch righ
now" to "Custom... batch".
Week 13:- On page 7 in the middle of the page frop the section
after
the % demo13 line about changing the emulator.
Add the following words to the first sentence in step 4 of the
exercise.
MSF file and your toFasta format file as well from
Add the following mv line after the one already given.
% mv ../eleven/*.tfa .
At the top of page 8 change the last line in the first paragraph to
read.
My example follows; this is only an example, we will not be using
tophylip in this exercise.
At the top of page 11 change the last sentence in the paragraph to
read.
A screen trace of my session is given below, run your tfa
file through the program.
In the readseq screen trace, change the name of the file used to
ef.tfa and use this as a guide from your own running of the
program.
On page 19 in the middle change the mv lines to read as follows.
% mv outfile ef_kim_prodist.fitch
% mv treefile ef_kim_prodist.fitch_tree
The following is a listing of the typos found in the BC/BP 378 html
versions of the manuals for the fall 97.
Week 5:- At the top of page 10, draw in single bonds between
the two nitrogens of the histidine ring and carbon between them.
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.]
97 changes include:-
- 1) The use of RasMol for all non-modelling demos throughout the
course.
- 2) The rearranagement of various exercises to fit the testing schedule
better.
- 3) The manuals were printed as doubled sized pages for the first
time.
96 changes include:-
- 1) Conversion of the course from a VMS to UNIX platform.
- 2) Adding hard copy images of items covered in the demos.