Generating alignments of genetic sequences

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Abstract
Molecular biologists have recently developed the technology required to determine the genetic information of complete organisms. They are now faced with a number of interesting computational problems as they attempt to process data. We are interested in developing a software environment to support molecular biologists. As their computational problems are frequently complex and computation-intensive, we believe that such an environment must both support rapid prototyping of new algorithms and allow high performance execution on a variety of multiprocessor configurations. We believe that this can be achieved using a bilingual approach, in which the upper levels of programs are coded in a concurrent logic programming language and the lower levels in C. The concurrent language provides ease of parallel programming and portability over a range of parallel computers; C provides efficient implementation of low-level algorithms. To explore the suitability of this approach, we have investigated its use in attacking a prototypical computational problem, the problem of aligning a set of sequences of genetic material. This report introduces the algorithm used to generate alignments, outlines the techniques used to develop the bilingual program, and describes initial experiments in parallel execution of this program. 7 refs., 2 tabs.

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