Multi-Purpose Parallel Process for Biosequence Analysis

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This project is building an application-specific computer system for biosequence comparison. The architecture is suitable for a wide range of sequence comparison methods, including the Smith- Waterman algorithm, BLAST, profile searches and dictionary methods. In addition, the architecture is being integrated with software for the statistical analysis of sequences using techniques such as hidden Markov models. The core of the architecture is a linear array of SIMD processing elements, each with a small local memory. A single chip can contain 64 of these elements, so a board with 20 chips will hold 1280 processors. The processing elements have been tuned to sequence comparison by incorporating a single cycle add-and-min instruction and a data-path for quickly recording the results of the instruction. Software, I/O, and algorithms have been considered in the design of this architecture; the resulting balanced implementation should result in high performance at low cost.