Course Materials for Bioinformatics I
Fall 2002


  • What is Bioinformatics I?
  • Basic Definitions
  • Useful Websites
  • Readings
  • Nucleic Acids Research 2002 Database Issue
  • Bioperl paper
  • Study guide for exam: part 1 and part 2.


  • assignment #1
  • assignment #2
  • assignment #3

    Class notes:

  • Notes on the genome paper in Nature.
  • Notes about PipMaker.
  • Notes about extensions to PipMaker.
  • Paper on UCSC Genome Browser. The Browser itself.
  • Users guide to the human genome. Published in Nature Genetics, September 2002.
  • Alignment scores and PSI-Blast
  • NCBI: paper and website
  • Ensembl: paper and website
  • notes on dynamic programming
  • outline of the Blast program
  • paper on Gapped Blast and PSI Blast
  • amino acid substitution scores
  • probabilistic sequence models
  • probabilistic sequence models, part 2
  • simple example of Viterbi decoding
  • paper on GenScan

    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.