A CMOS architecture allowing parallel DNA comparison for on-chip assembly

This paper introduces a CMOS based system that has been designed to allow parallel comparison of fragmented DNA sequences for on-chip assembly. The compatibility of different existing PC-based algorithms for implementation in CMOS is compared and the overlap-layout-consensus approach is found to be the most suitable one. The designed system comprises a scalable processing array capable of parallel computation, which allows identification of overlaps in DNA fragments in addition to error tolerance through dynamic programming. Analysis shows that there is a “pixel area vs computation time” trade-off when implementing such a parallel architecture. Results from a hypothetical assembly confirm good overlap detection and error tolerance, with up to 94% similarity in the detected overlaps, when the error is as much as 10%.