8/25 syllabus
8/27 lecture
1
reference
material
9/1 lecture
2
9/3 lecture
3
9/8 lab1
9/10 lecture
4
9/15 lecture
5
9/17 lecture
6
9/22 lecture
7
9/24 lecture 8 - continue of lecture 7
Project
1
testing
Project
2
testing
Project
3
testing
mid-term date: postponed to 11/3/04 (Wed.) in class
Grading
Guide
Extra credit (10%)
If you are considering getting extra credit, you must do the following
for all
the remaining four presentations:
1. Write at least one questions on paper and hand it in to me before
the
presentation.
2. Ask one question to the speaker in class
3. Do the extra credit homework about paper 2 to 6. It contains
questions that
are mostly compiled from the questions asked in class.
Paper list:
1. "Fast Algorithms for large -scale
genome Alignment and Comparison" Delcher
A. L., Phillippy A., Carlton J., Salzberg
S. Nucleic Acids Research 30(11) p2478-83 (2002)
2. "Gapped BLAST and
PSI-BLAST: a new generation of protein
database
search programs" Altschul et al. Nucleic
Acids
Research, 25(17) p3389-402 (1997)
3. "Assembly of Protein Tertiary Structures
from Fragments
with Similar Local Sequences using Simulated Annealing and Bayesian
Scoring
Functions" Simons K.T., Kooperberg C.,
Huang E.,
Baker D. Journal of Molecular Biology 268 p209-25 (1997)
4.
"Comparative Protein Modelling by Satisfaction of Spatial Restraints"
Sali A. and Blundell T, Journal of Molecular Biology (234), 779-815
(1993)
A couple of issues that might affect your decision making.
1. There will be a homework related to paper 1
2. To make the weight about the same for all the
papers,
whoever presents paper 6 will need to expand a little bit because the
method is
not totally discussed in this paper. Paper 6 is shorter than others,
and that
is why you need to extend beyond this paper a little bit.