Table 1.
Online databases
| Resource | Description | Web address |
| GenBank | Searchable database of protein and DNA sequences, based in the U.S. | http://www.ncbi.nlm.nih.gov/Genbank/index.html |
| Human Genome Browser | Visual way to examine chromosomal segments of varying sizes. Sequence information is available, as are other annotations and genome comparisons. | http://genome.ucsc.edu/cgi-bin/hgGateway?org=human |
| Ensembl | European repository for many genome projects. Very user-friendly and good graphic displays. | http://www.ensembl.org/ |
| Function Junction | A convenient site to learn functional information about yeast genes and ORFs. | http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction |
| GeneOntology | A consortium that is unifying terminology used to describe genes and their cellular roles in all species. | http://www.geneontology.org/ |
| MIPS | Searchable database of the molecular structure and functional network of Saccharomyces cerevisiae. | http://mips.gsf.de/proj/yeast/CYGD/db/index.html |
| ExPASy (Expert Protein Analysis System) | Proteomics database hosted by the Swiss Institute of Bioinformatics with information about protein sequences, structures and 2-D PAGE. | http://us.expasy.org/ |
| Protein Data Bank | Respository of all protein structures that is searchable by protein names and key words. | http://www.rcsb.org/pdb/ |
| CATH Protein Structure Classification | Hierarchical classification of protein domain structures that clusters proteins at four major levels, class (C), architecture (A), topology (T), and homologous superfamily (H). | http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html |
| DIP: Database of Interacting Proteins | Searchable database that shows protein–protein interactions based on experimental and computational information. | http://dip.doe-mbi.ucla.edu/ |
| PathCalling | Searchable proteome-wide analysis of yeast protein interactions using yeast two-hybrid screens. | http://portal.curagen.com/extpc/com.curagen.portal.servlet.Yeast |
| Osprey | Nice graphical representation of physical and genetic biological interactions; requires special plug-in or can function as a stand-alone program. | http://biodata.mshri.on.ca/osprey/servlet/Index |
| Stanford Microarray Database | Provides raw and normalized data from microarray experiments, their corresponding image files and interfaces for data retrieval, analysis, and visualization. Excellent source for students to explore. | http://genome-www5.stanford.edu/MicroArray/SMD |
| GEO: Gene Expression Omnibus | Gene expression and hybridization array data repository with methods for searching and visualizing results. | http://www.ncbi.nlm.nih.gov/geo/ |
| Expression Connection | Yeast database searches the results of several microarray studies for gene expression data for a given gene or ORF. Source for Figure 6. | http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl |
| ArrayExpress | Searchable British public repository for microarray-based gene expression data. | http://www.ebi.ac.uk/arrayexpress/ |
| The SNP Consortium | A public/private database containing about 1.8 million SNPs (single nucleotide polymorphisms). | http://snp.cshl.org/ |
| Alternative Splicing ASAP | Searchable database with graphical presentations of alternative splicing. | http://www.bioinformatics.ucla.edu/ASAP/ |
| MHC Haplotype Project | A work in progress that will provide the complete genomic sequences of at least eight different HLA-homozygous typing haplotypes. | http://www.sanger.ac.uk/HGP/Chr6/MHC/ |
| PNAS: Proceedings of the National Academy of Science, USA | Provides free access to all papers 6 months after publication. Same policy used by Science. | http://www.pnas.org/ |
| PubMed Central | U.S. National Library of Medicine's digital archive of life sciences journal literature with free access. | http://www.pubmedcentral.nih.gov/ |
| HighWire Press | Largest repository of free online journals with varying periods of delay before freely available. | http://highwire.stanford.edu/lists/freeart.dtl |