Course Materials for Bioinformatics I
Fall 2003

  • Study guide for exam: part 1


  • What is Bioinformatics I?
  • Basic Definitions
  • Useful Websites
  • 2003 NAR Database Issue
  • 2003 NAR Website Issue
  • Nature Genome Gateway

    Class Notes:

  • local copy of public human genome paper (PDF)
  • local copy of mouse genome paper (PDF)
  • Genome Headlines
  • Paper on UCSC Genome Browser. Two images showing inter-species sequence conservation. The Browser itself.
  • Papers on GenBank and NCBI.
  • Notes about PipMaker; more notes about PipMaker; PipMaker publication; MultiPipMaker publication.
  • Notes about alignments scores and Psi Blast.
  • Notes the dynamic-programming algorithm for aligning two sequences.
  • Blast outline and paper on Gapped Blast and PSI Blast.
  • Recent short paper about Clustal.
  • amino acid substitution scores
  • probabilistic sequence models
  • Hidden Markov Models


  • assignment #1