The current deluge of genomic sequences has spawned the creation of tools 
capable of making sense of the data. Computational and high-throughput 
experimental methods for generating links between proteins have recently been 
emerging. These methods effectively act as hypothesis machines, allowing 
researchers to screen large sets of data to detect interesting patterns that can 
then be studied in greater detail. Although the potential use of these putative 
links in predicting gene function has been demonstrated, a central repository 
for all such links for many genomes would maximize their usefulness. Here we 
present Predictome, a database of predicted links between the proteins of 44 
genomes based on the implementation of three computational methods--chromosomal 
proximity, phylogenetic profiling and domain fusion--and large-scale 
experimental screenings of protein-protein interaction data. The combination of 
data from various predictive methods in one database allows for their comparison 
with each other, as well as visualization of their correlation with known 
pathway information. As a repository for such data, Predictome is an ongoing 
resource for the community, providing functional relationships among proteins as 
new genomic data emerges. Predictome is available at http://predictome.bu.edu.