BSCI 380 - Comparative Bioinformatics

Homework 2006

Assignment 1 (20 points)

Use the Smith-Waterman algorith to align these two amino-acid sequences:

a: SRGMIEVGNQWT

b: RGMVVGRW

Use a BLOSUM62 matrix and a monotonic gap penalty of 8 (i.e., use the same penalty for gap creation and extension). Show the calculated value for each cell, which of the four possible functions yielded the best score, the traceback, and the final alignment.

Reading

Textbook, chapters 1-5 (by Midterm 1).

Cohen, J.E. 2004. Mathematics is biology's next microscope, only bettter; biology is mathematics' next physics, only better. PLOS Biology 2:e439.

Gill, S.R., Pop, M., DeBoy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., Gordon, J.I., Relman, D.A., Fraser-Liggett, C.M., and Nelson, K.E. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.

Fraser, C.M., Casjens, S., Huang, W.M., Sutton, G.G., Clayton, R., Lathigra, R., White, O., Ketchum, K.A., Dodson, R., Hickey, E.K., Gwinn, M., Dougherty, B., Tomb, J.F., Fleischmann, R.D., Richardson, D., Peterson, J., Kerlavage, A.R., Quackenbush, J., Salzberg, S., Hanson, M., vanVugt, R., Palmer, N., Adams, M.D., Gocayne, J., Weidman, J., Utterback, T., Watthey, L., McDonald, L., Artiach, P., Bowman, C., Garland, S., Fujii, C., Cotton, M.D., Horst, K., Roberts, K., Hatch, B., Smith, H.O., and Venter, J.C. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580-586.

Textbook, Chapters 10-16 (by Midterm 2).

Hendrik N. Poinar, Carsten Schwarz, Ji Qi, Beth Shapiro, Ross D. E. MacPhee, Bernard Buigues, Alexei Tikhonov, Daniel H. Huson, Lynn P. Tomsho, Alexander Auch, Markus Rampp, Webb Miller, and Stephan C. Schuster (2006) Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science. 311: 392-394

Platt, J.R. (1964) Strong Inference. Science. 146: 347-353.

Pop, M., A. Phillippy, et al. (2004). "Comparative genome assembly." Briefings in Bioinformatics 5(3): 237-248.

Marcel Margulies, Michael Egholm, William E. Altman, Said Attiya, Joel S. Bader, Lisa A. Bemben, Jan Berka, Michael S. Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B. Dewell, Lei Du, Joseph M. Fierro, Xavier V. Gomes, Brian C. Godwin, Wen He, Scott Helgesen, Chun He Ho, Gerard P. Irzyk, Szilveszter C. Jando, Maria L. I. Alenquer, Thomas P. Jarvie, Kshama B. Jirage, Jong-Bum Kim, James R. Knight, Janna R. Lanza, John H. Leamon, Steven M. Lefkowitz, Ming Lei, Jing Li, Kenton L. Lohman, Hong Lu, Vinod B. Makhijani, Keith E. McDade, Michael P. McKenna, Eugene W. Myers, Elizabeth Nickerson, John R. Nobile, Ramona Plant, Bernard P. Puc, Michael T. Ronan, George T. Roth, Gary J. Sarkis, Jan Fredrik Simons, John W. Simpson, Maithreyan Srinivasan, Karrie R. Tartaro, Alexander Tomasz, Kari A. Vogt, Greg A. Volkmer, Shally H. Wang, Yong Wang, Michael P. Weiner, Pengguang Yu, Richard F. Begley, Jonathan M. Rothberg (2006). Genome sequencing in microfabricated high-density picoliter reactors. Nature. 437: 376-380.

Supplementary Readi

Robert D. Fleischmann; Mark D. Adams; Owen White; Rebecca A. Clayton; Ewen F. Kirkness; Anthony R. Kerlavage; Carol J. Bult; Jean-Francois Tomb; Brian A. Dougherty; Joseph M. Merrick; Keith McKenney; Granger Sutton; Will FitzHugh; Chris Fields; Jeannie D. Gocyne; John Scott; Robert Shirley; Li-Ing Liu; Anna Glodek; Jenny M. Kelley; Janice F. Weidman; Cheryl A. Phillips; Tracy Spriggs; Eva Hedblom; Matthew D. Cotton; Teresa R. Utterback; Michael C. Hanna; David T. Nguyen; Deborah M. Saudek; Rhonda C. Brandon; Leah D. Fine; Janice L. Fritchman; Joyce L. Fuhrmann; N. S. M. Geoghagen; Cheryl L. Gnehm; Lisa A. McDonald; Keith V. Small; Claire M. Fraser; Hamilton O. Smith; J. Craig Venter. (1995). Whole-Genome Random Sequencing and Assembly of Haemophilus Influenzae Rd. Science. 269: 496-498.

Eddy, S. R. (2004). "What is a hidden Markov model?" Nature Biotechnology 22(10): 1315-1316.