Part one of the final exam is now posted! Part one is due Friday, May 8 at noon.

The final will in two parts: an in class part held in the computer lab from 8-9 AM Friday, May 8 and a take home part that I will post Wednesday and that will be due Friday, May 8 at noon.

Lab 13 on Friday 5/1/09 will be optional and can be turned in for extra credit.

Reading assigned: Understanding Bioinformatics: Ch. 16

Reading assigned: Understanding Bioinformatics: Ch. 15.1

Reading assigned: Understanding Bioinformatics: Ch. 10

Test this Friday! 2-4 pm in the computer lab (Nursing building).

Audio recording of Lecture 6b (Scoring matrices): mp3

Reading assigned: Understanding Bioinformatics: Ch. 9

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

Listening assigned: Eric Lander lecture on Genomics at MIT

Reading assigned: Understanding Bioinformatics: Ch. 8

FYI: ab initio protein folding projects that can contribute to be running them on your computer: Folding@Home, Docking@Home, Rosetta@Home

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

Reading assigned: Understanding Bioinformatics: Ch. 11.1-3, 11.7, 12.1, Ch 14

Reading assigned: Understanding Bioinformatics: Ch. 13, NCBI structure primer

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

Protein folding as a game! Foldit from the University of Washington Baker lab (and CS Dept.) I found it fun and addictive.

Reading assigned: Understanding Bioinformatics: Ch. 1.3, 9.1-9.6

Test this Friday, 2-4 pm in the computer lab (Nursing building).

The Lab 4 deadline is Thursday 2/12.

Audio recording of Lecture 6: mp3

Audio recording of Lecture 5b: mp3

Audio recording of Lecture 5a: mp3

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.

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

The original Lab 3 has been restored. You can turn in answers to any combination of the two versions. I don't want you to have to redo any completed questions.

The Lab 3 deadline is Thursday 2/5.

The Lab 2 deadline is Thursday 1/29.

Audio recording of Lecture 4: mp3, WAV

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

Audio recording of Lecture 3: mp3, WAV

Reading assigned: Understanding Bioinformatics Ch. 3.

Reading assigned: Understanding Bioinformatics Ch. 1 and 2.

Please read the syllabus--it contains answers to most initial questions.