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
- Making Sense of DNA and Protein Sequence Analysis Tools
(PowerPoint 2.3Mb Jul 21 08)
- GeneScan Predicts protein sequence, location of exons, start and stop codons from a nucleotide sequence.
- ScanProsite Identifies potential functional domains in an amino acid sequence.
- BLAST Searches databases for nucleotide or amino acid sequences similar to your own.
- GenBank Database
of all publicly available DNA sequences.
- More bioinformatics links:
- Model of
NCBI Entrez Databases
- Intro to NCBI Mapviewer (Microsoft Word 171kB Jul18 08)
- Intro to NCBI Entrez SNP (Microsoft Word 207kB Jul18 08)
- Intro to NCBI OMIM (Microsoft Word 176kB Jul18 08)
- Intro to NCBI COGs (Microsoft Word 643kB Jul18 08)
- Intro to NCBI Entrez Geo (Microsoft Word 921kB Jul18 08)
ModelingRanyee Chiang Presentation on Modeling (PowerPoint 7.9MB Jul20 08)
ModBase Database of Protein Structures
- 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
- 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.