Nucleic acid and protein sequences contain a wealth of information of interest to molecular biologists. The advent of molecular sequence databases provides a unique opportunity for the computer analysis of all available sequences. Sequence databases serve two main functions: (i) to facilitate comparisons with newly determined sequences, and (ii) to act as a source of data for the generation and testing of hypotheses concerning molecular sequence organisation and evolution. The large amounts of sequence data now becoming available require that algorithms for database searching be fast and efficient and considerable progress is being made in this area.