These studies are somewhat hampered by the slow run-times of these structure comparison techniques. Thus, the data sets on which the run tend to be small. However, this is too much to hope for. Thus, we consider the problem of providing a tool which speeds up proximity searching for an arbitrary metric. Thus, our methods, which we call SparseMap yields a tradeoff between speed and generality.
Many open problems remain.
In particular, SparseMap proceeds by embedding the underlying metric into a low-dimensional Euclidean space, and then using Euclidean methods for the actual similarity search. Literature Searching and Protein Similarity. Bioinformatics has heretofore been mainly concerned with structure and sequence. We propose that a third data type, literature, is an untapped resource for automaticall explicating biological relationships. The explosion of biological data has occurred at a time when the Internet is ubiquitous in the research community.