CSE 527,  Au '07:  Computational Biology

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2006 Lecture Notes 1. Overview:  source pdf 2. Global Alignment:  source pdf 3. Local Alignment; DNA replication:  source pdf 4. Blast; Statistics:  source pdf 5. Alignment Scores; PCR:  source pdf 6. MLE; Sequencing:  source pdf 8. TF Binding; Weight Matrices:  source pdf 9. MEME & Gibbs Sampler:  source pdf 10. Motif Comparison; Phylogeny:  source pdf 11. Phylogenetic Footprinting; HMMs:  source pdf 12. Hidden Markov Models, II:  source pdf 13. Pfam; Genes & Splicing:  source pdf 14. Gene Finding, II:  source pdf 15. RNA Roles & Structure:  source pdf 16. RNA Secondary Structure; CMs:  source pdf 17. Covariance Models, II:  source pdf 19. CMs IV: CMfinder:  source pdf 20. Phylogeny & Pfold:  source pdf 21. Pfold:  source pdf

Note Taking: One of the course requirements is that each student act as ``scribe'' for one or two lectures. I do grade them, but only lightly, on a no credit/check/check plus scale. Your job is to produce a legible set of notes for that lecture that I can put on the web for the benefit of the rest of the class. My slides will also be available on the web, so there's no need to reproduce those, but you can give more background on the problems being addressed, the methods covered, fill in details I talked about in class that aren't on the slides, summarize in-class discussion, add extra figures or pictures, add references, suggest exercises or further reading, etc. Basically anything that might help people learn the material. At left are links to previous year's notes. Lecture boundaries won't match exactly, and I won't cover all the same material, but to the extent that I do, you may use these notes as a starting point, and refine them. Links to the "source" files are given, as well as PDF's; feel free to down load and edit them. (If you do, leave the original author's names on it, but add your own.) If the original was more than one file (e.g. a text file plus a figure or two) then they are bundled together as a single .zip file; let me know if you have trouble unpacking them. I don't care too much about format, basically anything I can turn into PDF is ok. Old ones are in a mix of LaTeX, Word, html, rtf, plain text etc. There might even be a Mathematica notebook. Typical notes are 3-5 pages. I prefer readable prose to outlines or bullet points. Email your notes to me (ruzzo at cs) when you've finished. Please try to do it within one week of class, and please give me a PDF plus your source file(s), including figures, non-standard Latex macros if any, etc., so that I can reconstruct a PDF if I edit anything.

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