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.

AliMac is an implementation of a sensitive sequence alignment algorithm on a parallel computer. The method achieves reliable alignments for very distantly related sequences from a combined use of amino acid exchange weights and physicochemical characteristics. The algorithm is computing intensive and its usage on conventional computers is limited to a relatively small number of sequences. The parallel implementation uses a Macintosh IIcx host computer and 21 transputers and achieves 22 times the speed of a VAX 8650 at a fraction of the cost. This paper describes the AliMac hardware and software and discusses problems and peculiarities of parallel implementations, especially with transputers. Finally, several popular sequence alignment algorithms are compared in their ability to detect distantly related sequences in searching large databases.