Final Exam this Wednesday! 10AM - 12 noon in the computer lab.

Reading assigned: Understanding Bioinformatics Ch 15.2.

Reading assigned: Understanding Bioinformatics Ch 16.

Reading assigned: Understanding Bioinformatics Ch 15.1.

Exam II this Friday! 2-4 pm in the computer lab.

Reading assigned: Understanding Bioinformatics, remainder of Ch 9 & 10.

Reading assigned: Understanding Bioinformatics Ch 10.2, 10.4, 10.6-8

Reading assigned: Understanding Bioinformatics Ch 1.3, 9.1-9.6

Reading assigned: GENE SEQUENCING: The Race for the $1000 Genome html, pdf

Listening assigned: Eric Lander lecture on Genomics at MIT

Reading assigned: Ch 6 from Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Ed. by Baxevanis and Ouellette.

Protein folding as a game! Foldit from the University of Washington Baker lab (and CS Dept.) I found it fun and addictive. The initial learning problems are a good way to get a feel for visualizing protein structure.

CASP (Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction), look under 'Results': CASP8. All the groups did a terrible job predicting structure T0405 and most did a good job on the first structure, T0388-D1.

Interesting paper on caspase 12 evolution: Xue et al., 2006

Exam this Friday! 2-4 pm in the computer lab. Covering lectures 9 to 17 (proteins, sequencing, and gene annotation).

Reading assigned: Understanding Bioinformatics Ch. 8.

Reading assigned: Understanding Bioinformatics Ch. 7.

Reading assigned: Understanding Bioinformatics Ch. 6.1.

For preparing alignments for publication, the BOXSHADE program is one option. It prepares B&W images. (BOXSHADE server, download). The AMAS and Alscript programs can also produce publication figures.

Reading assigned: Understanding Bioinformatics Ch. 6.4, 6.5, and 6.6.

Reading assigned: Understanding Bioinformatics Ch. 5.1, get what you can out of 5.2, 5.4

Reading assigned: Understanding Bioinformatics Ch. 4.1-4.7

Reading assigned: Understanding Bioinformatics Ch. 3.

Reading assigned: Understanding Bioinformatics Ch. 1 and 2.

Chapters 1, 4, & 7 of the textbook are available on the publisher's website: link