Genomics and Bioinformatics Resources

Participants in a 2008 workshop shared these presentations and resources related to teaching genomics in undergraduate courses.

Looking at Whole Chromosomes and Genomes

Bioinformatics Tools

NCBI Resources

Protein Structure


Ranyee Chiang Presentation on Modeling (PowerPoint 7.9MB Jul20 08)
ModBase Database of Protein Structures

Internet Resources

Seminal Papers

  • Sippl, M. J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213, 859-83 (1990).
  • Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.J Mol Biol. 1987 Feb 20;193(4):775-91.
  • Sali, A. and Blundell, T.L., Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 1993. 234: p. 779-815.
  • A method to identify protein sequences that fold into a known threedimensional structure. J. U. Bowie, R. Luthy, D. Eisenberg. Science 253(5016): 164-70

Alignment Programs

  • Base-By-Base Download from http://athena.bioc.uvic.ca/. A user-friendly graphical interface for sequence alignments. It aligns sequences using Clustal or T-coffee, you can color the alignment, edit it, annotate.
  • MultAlin Protein sequence alignment.

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