Supplementary Reading, CAP 5510, Spring 2007

• Popular Articles
  • California Sea urchin genome sequenced, Nov 2006.
  • SIDS among Amish community, October 2004.
  • Molecular Biology: made simple and fun, Cache River Press.
  • CARTOONS!
• Introductory Molecular Biology
  • Human Genome Program, U.S. Department of Energy, Primer on Molecular Genetics, Washington, D.C., 1992. Prepared by Denise Casey, Human Genome Management Information System, Oak Ridge National Laboratory, for the 1991-92 DOE Human Genome Program Report.
  • An animated primer on the basics of DNA, genes, and heredity., 2002 Merlot Classics.
  • Dolan DNA Learning Center Multimedia Guides to Molecular Biology.
  • DNA seen through the eyes of a coder
  • About the Human Genome Project
  • (Publicly Funded) Human Genome Draft and Nature Website 
  • Multimedia Presentations and descriptions of many Molecular Biology techniques and concepts: The Human Genome Project
• BLAST
  • Original BLAST paper by Altschul, Gish, Miller, Myers, and Lipman Basic Local Alignment Search Tool, J. Mol. Biol. (1990) 215, 403-410.
  • How to use BLAST: BLAST information. Also includes a tutorial on BLAST, and a lot of related material.
  • How BLAST works: Chapter titled The BLAST Sequence Analysis Tool, by Tom Madden from NCBI Handbook.
  • Tutorial on The Statistics of Sequence Similarity Scores, by S. Altschul.
  • Recent paper on BLAST by McGinnis and Madden: BLAST: at the core of a powerful and diverse set of sequence analysis tools, Nucleic Acids Res. 2004, 32(Web Server issue):W20-5.
  • BLAST variants: Paper by Altschul, Madden, Schaffer, Zhang, Zhang, Miller, Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs , Nucl. Acids Res. (1997) 25:3389-3402.
• Hidden Markov Models
  • An excellent treatment of Hidden Markov Models can be found in the book "Biological Sequence Analysis", by Durbin, Eddy, Krogh, Mitchison, Cambridge University Press, 1998. In particular, chapters 1-3 introduce the basics. Applications to sequence alignments can be found in chapters 4-6. It also has a chapter on the relevant "Background on Probability" (chapter 11), which I also recommend very highly.