Date	Topics	Slides/Lecture notes	Add'l resources
1/24	Introduction Molecular biology primer	Lecture 1 Homework 1
1/29	Molecular biology primer Perl/Perl Modules	Lecture 2
1/31	Perl/Perl Modules/BioPerl	Lecture 3
2/5	Bioinformatics Databases	Lecture 4
2/7	Bioinformatics Databases	Lecture 5 Homework 2
2/12	Sequence alignment - exact matching	Lecture 6
2/14	Sequence alignment - suffix trees/suffix arrays SNOW DAY
2/19	Sequence alignment - inexact matching	Pevzner 6.4-6.10 Lecture 8
2/21	Sequence alignment - heuristics	Lecture 9 Project 1 handed out	BLOSUM62 matrix Sample input file Sample database Sample parameters Sample output
2/26	Multiple sequence alignments	Pevzner 6.10 Lecture 10
2/28	Construction of phylogenetic trees	Pevzner 10.5-10.12 Homework 3 Lecture 11
3/5	Tree analysis/Tree display	Lecture 12
3/7	Suffix trees Suffix arrays	Pevzner 9.4-9.5 Lecture 13	Reminder: Daylight Savings Time ends on Sunday!
3/12	Genome sequence assembly	Pevzner 8.3-8.9 Lecture 14
3/14	Genome sequence assembly	no homework handed out Lecture 15
3/19	Spring break
3/21	Spring break
3/26	Lessons from project 1 Dynamic programming recap	Project 1 due Lecture 16
3/28	Gene finding	Pevzner chap. 11 Lecture 17
4/2	Midterm	Passover - no homework handed out or due
4/4	Midterm recap/Gene finding	Project 2 suggestions "Lecture" 18
4/9	Gene finding	Pevzner chap. 11 Project 2 handed out Lecture 19	Project 1 evaluation criteria smalltest-query.fa smalltest-db.fa bigtest-query.fa bigtest-db.fa swaptest.fa BLOSUM80 fastaout.txt
4/11	Microarrays and data clustering	Pevzner chap. 10 Lecture 20 Homework 4	Project2 details
4/16	RNA structure prediction	Lecture 21
4/18	Open-source	Richard Stallman's talk @ 4 1115 CSIC
4/23	Protein structure prediction	Lecture 22
4/25	Protein structure prediction Proteomics	Lecture 23
4/30	Mass Spectrometry Gene Networks	Pevzner chap 8 Lecture 24
5/2	Real-life examples	Lecture 25
5/7	Recap/Review	Project 2 due!!
5/9	Recap/Review Final thoughts
5/15	Final exam	1:30-3:30pm CSIC 3120