Prior Class Notes
NOTE: THESE ARE THE NOTES FROM PREVIOUS TIMES I TAUGHT CS 124,
MOSTLY FROM 2002, WITH SOME FROM 2003, 2005 and 2006.
THEY ARE MADE AVAILABLE TO HELP
YOU READ AHEAD. NOTE THAT THE DATES MAY NOT CORRESPOND TO LECTURE DATES IN 2008, BUT ARE CLOSE. I MAY ALSO BE ADDING TO AND MODIFYING THESE SOMEWHAT.
WHEN I DO, I WILL PUT THOSE IN THE ``CURRENT NOTES" SECTION.
Some class materials are currently ID and password protected. I will be removing that, but in case it happens that you are asked for an ID and a password, the current ID is cs124 and the current password is forgetmenot
- Lecture #1, Monday April 1 [ (pdf) ]
- Lecture #2, Weds. April 3 [ Lecture 2 in pdf ]
- Lecture #3, Frid April 5 [Acrobat]
- Lecture #4 Monday April 8 [Acrobat]
- Lecture #5, Weds. April 10 [Acrobat]
- Lectures #6, #7, Friday April 12 and Monday April 15 [Acrobat]
- Lecture #8, Wed. April 17 Simplified Smith-Waterman discussion (pdf)
A full and formal discussion of local alignment (pdf),
A full and formal discussion of local alignment (ps)- Lecture #9, Friday, April 19 Intro to Statistical Issue and Expected length of longest common subsequence pdf
- Lectures #10, #11 Monday April 22, Weds. End-gap-free alignment April 24 (pdf)
- Lecture #12, Friday April 26 Expected length of the longest common substring (pdf)
- Lectures number 13, 14, 15, 16 from April 29 to May 8 Short note
- Lecture 17, May 10, 2002
And notes on the granin story etc. (pdf)
- Lectures 18, 19, 20 MAY 15, 17, 20 2002
Lecture notes on global multiple alignment. There is more material in these notes than we actually discussed in class, particularly the proofs of several claims we made in class but didn't prove. So skim the notes and only read in detail the things we coverd in class, and what else is of particular interest to you. [Acrobat]
- Lectures 21, 22 May 22, 24 PSSMs, profiles and profile-based scoring(pdf)
See also the notes posted below (in 2006) on aligning a sequence to a profile and/or a multiple alignment.
- Lectures ?
I don't know what lecture we are on, but for the last several lectures we have been talking about Hidden Markov Models, using the notes distributed in class, so nothing to post here.
Lectures ? June 5, 7 2002
We discussed PSI-Blast a bit, and you have notes on it in an earlier lecture.
Then we started talking about evolutionary and ultrametric trees. Notes for that are in [Evolutionary Trees]
New Class Notes 2003 New Class Notes 2005 More Class Notes, Posted 2006 More Class Notes, Posted 2008 Class Notes for Professor Koehl's LectureMay 15, 2008 Notes on aligning three seqeuences, Posted 2008
[
Final exam from 2005 ]
[
Final exam from 2006 ]
Sorry, I don't have any answers to these specific final exam questions.
Also, the 2008 final exam will have one question on Perl, testing material learned since
the midterm.
Lecture Videos: Synopses of the videos These will be augmented as the course proceeds.
Details on how the Lecture Notes and Class Videos correspond to the
lectures given in the class in 2008. These will be augmented as the course proceeds.
Recommended Papers Announcements Resources Appendices
[
Notes on aligning a string to a profile]
[
Notes from the May 6, 2008 lecture - rant on how to misuse probability]
[
Koehl May 15, 2008]
[
Exact DP for sum of pairs criterion for three sequences.
These are lecture videos taken in 2002. I will provide an index of the lectures as we go along, but they
roughly correspond to the order of the lectures this year. However, not all lectures that will be given this year will
correspond to lectures in 2002, and conversely, there are lectures there that cover material
we will not cover. Be aware that in the first lecture, where the URL for the 2002 class is given, and the
password for access to class material is given, those are no longer correct. See the 2008 material for that information.
