Course Materials for BMMB/CSE 597D
Spring 2000

Schedule for April 24-28.


  • What is BMMB/CSE 597D?
  • Basic Definitions
  • Useful Websites
  • Readings

    Class notes:

  • interspersed repeats
  • dynamic-programming sequence alignment. PostScript or PDF
  • Blast. PostScript or PDF
  • greedy alignment algorithms. PostScript or PDF
  • GenScan. PostScript or PDF
  • fundamental methods for HMMs. PostScript or PDF
  • matrices of substitution scores. PostScript or PDF

    Necessary software: Some of the materials will be presented as PostScript and PDF documents, so you will need to handle at least one of these formats. If your system doesn't already have one, you may want to fetch and install a free PostScript/PDF viewer manufactured by Aladdin Inc, called Ghostscript. The Aladdin web page has instructions for attaching it to Netscape or MS Internet-Explorer. Another popular program for reading PDF files is Adobe Acrobat Reader.

    You might find it amusing to learn how I got involved in bioinformatics.