Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer.

An implementation of Profilesearch (a technique to search for relationships between a protein sequence and multiply aligned sequences) for a parallel computer is described. The number-crunching machine, consisting of 21 T800 transputers, is connected to a Macintosh IIcx host computer. The program utilizes a standard Macintosh application as its user-interface, resulting in a transparent and user-friendly environment for addressing the parallel computer. The program is independent of the number of available processors and exceeds the speed of a VAXstation 3200 with only one transputer in operation, thus allowing cheap and fast database searches with a PC front-end. For a larger number of processors, the speed increase is approximately linear with no obvious symptoms of saturation with the available maximum of 21 transputers. The program and environment are useful to search quickly and easily for similarities between a single sequence or sequence set and individual sequences contained in a large database. The alignment is determined by typical dynamic programming techniques.