Fall 1998-1999
Algorithms in Molecular Biology 0368.4020.01

Ron Shamir

Sundays 16-19 Schreiber 12

Contact Info:

		Email	Phone	Office	Office Hours
Instructor:	Ron Shamir	shamir	640-9094	Schreiber 016	Thursday 17-18
TA:	Itsik Pe'er	izik	640-8979	Open Space	Thursday 13-14

Class B-board: (Last update: Mar 10 1999)

Course Outline:

Note: If you have a choice, we recommend that you use the ps files. The other file formats may miss certain figures and distort some formulas.

Lect	Date	Topic	Notes (shaded=draft)				Speaker	Scribe	Remarks
1	6/12	Introductory Concepts	ps	ps.gz	pdf	html	Ron Shamir	Sigal Korczyn, Nimrod Hoffien	Russian translation
2	13/12	Pairwise alignment	ps	ps.gz	pdf	html	Ron Shamir	Eti Ezra, Guy Gelles
3	27/12	Sequence Alignment Heuristics	ps	ps.gz	pdf	html	Ron Shamir	Yossi Richter, Micky Frankel
4	1/1	Bioinformatics Tools	ps	ps.gz	pdf	html	Irit Orr	Irit Gat, Tal Kohen	Slides on DB-Searching (ppt html) and on Multiple Alignment (ppt html)
5	3/1	Multiple Sequence Alignment	ps	ps.gz	pdf	html	Ron Shamir	Itay Lotan, Ziv Modai
6	10/1	Hidden Markov Models	ps	ps.gz	pdf	html	Ron Shamir	Ron Wein, Nir Avrahami
7	17/1	Gene Finding	ps	ps.gz	pdf	html	Ron Shamir	Nadav Grossaug, Benny Ben-Ami
8	24/1	Protein Structure	ps	ps.gz	pdf	html	Haim wolfson	Itsik Mantin, Eyal Molad
9	31/1	Phylogeny	ps	ps.gz	pdf	html	Ron Shamir Itsik Pe'er	Gideon Shavit, Chaim Linhart
10	7/2	Physical Mapping	ps	ps.gz	pdf	html	Ron Shamir	Eran Yahav, Gaby Liron
11	14/2	Genome Rearrangements	ps	ps.gz	pdf	html	Ron Shamir Itsik Pe'er	Gil Arditi, Zivan Ori	Slides: ppt html
12	21/2	DNA Chips	ps	ps.gz	pdf	html	Ron Shamir	Dror Irony, David Oren

Handouts

• Course announcement
• Bibliograpy: textbooks, background and more.
• Assignment no. 1: Dynamic programming and sequence alignment (theory) ps, pdf, html
• Assignment no. 2: Sequence alignment in public databases (wet) ps, pdf, html
• Assignment no. 3a: Multiple sequence alignment and HMM (theory) ps, pdf, html
• Assignment no. 3b: HMM (practice) ps, pdf, html
• Assignment no. 4: Gene finding and Geometric Bioinformatics ps, pdf, html
• Assignment no. 5: Phylogeny, Physical Mapping, and Genome Rearrangements ps, pdf, html

Useful Links

• archive of the course , including lecture notes and references from previous years.
• links to related courses given worldwide.