Strategies for searching sequence databases.

We provide a detailed overview of the choices inherent in performing a sequence database search, including the choice of algorithm, substitution matrix and gap model. Each of these choices has implications that can be described as restrictions on the underlying model of sequence evolution, the expected degree of divergence between the query sequence and the database sequences (if one uses an evolutionary based matrix), as well as the sensitivity and selectivity of the search. We conclude with a series of recommendations for researchers performing these searches based on our experience and literature studies.

Information retrieval maps for biomedical research.

Integration of computer-based information sources should be useful for biomedical research. An information retrieval map is a graphical representation of a set of expert rules for integrating computer-based information sources based on the data connections among those information sources. The use and implementation of an information retrieval map for sequence alignment is described.

A simple approach for the distribution of computationally intense tasks in an heterogeneous environment: distribution of the MDPP image-processing package.

A method has been developed to link the display ability of a high-resolution graphics workstation with the computational power of a local mainframe or a remote supercomputer via an electronic data network. The method allows this link to be established in a manner largely transparent to the user. The application of the method is illustrated by our successful distribution of the computationally intensive portions of an imaging program (MDPP) from a small VAX workstation to a VAX mainframe and Cray Y-MP8/832 using a simple message-passing technique. This technique can be applied to almost any configuration of networked machines.