CS 5984: ALGORITHMS IN BIOINFORMATICS
Virginia Tech
Fall Semester, 2000

INSTRUCTOR

My weekly schedule is always here.

Graduate Teaching Assistant

SYLLABUS

COURSE CALENDAR

HOMEWORKS AND SOLUTIONS

OTHER RESOURCES

• Our textbooks:
  • Introduction to Computational Molecular Biology by Joao Carlos Setubal and Joao Meidanis, PWS Publishing Company, December 1996
  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Daniel M. Gusfield, Cambridge University Press, 1998

• Paper by Froger, et al., entitled Prediction of aquaporin function by sequence analysis. Includes a signature motif.

• Handouts of November 29, 2000:

  • Paper by Altschul, et al., entitled Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs.

  • Paper by Pearson and Lipman entitled Improved Tools for Biological Sequence Comparison. Discusses FASTA. Also available in Postscript.

• Handouts of October 30, 2000:

  • General information on BLOSSUM and PAM substitution matrices.
  • BLOSUM 45 similarity matrix.
  • BLOSUM 62 similarity matrix.
  • BLOSUM 80 similarity matrix.
  • PAM 30 similarity matrix.
  • PAM 70 similarity matrix.
  • An example multiple sequence alignment of 8 ESTs done with CLUSTALW.

• Find out what was on reserve in Newman Library.

• Also see the web site for the course CS 6104: Computational Biology.

Please report any problems found in these pages to: