Course Materials for Bioinformatics I
Fall 2004

Study guide for part of the final exam.
Study guide for remainder of the final exam.


  • What is Bioinformatics I?
  • Basic Definitions
  • Introduction to elements of biology -- cells, molecules, genes, functional genomics, microarrays
  • 2003 NAR Database Issue
  • 2003 NAR Web Server Issue
  • 2004 NAR Database Issue
  • 2004 NAR Web Server Issue
  • Introduction to sequence databasees

    Class notes and readings:

  • 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.
  • amino acid substitution scores
  • Methods to determine the number of clusters in a data set
  • Recent short paper about Clustal.
  • probabilistic sequence models
  • Hidden Markov Models
  • Genscan paper


  • assignment #1
  • assignment #2
  • phylogeny homework
  • HemoglobinMAC.nex
  • HemoglobinMAC.phy
  • HemoglobinPC.nex
  • HemoglobinPC.phy
  • hemoglobin_noalign_2004.txt
  • hemoglobin_noalign_2004.rtf

    Examples of class projects from 2004:

  • Protein modularity and evolution
  • Analysis of large deletions in human-chimp genomic alignments
  • Profile hidden Markov models
  • Comparison of drosophila genomes

    Some addional readings.