  Early hardware limitations of GPU (lack of synchronization primitives and
limited memory caching mechanisms) can make GPU-based computation inefficient.
Now Bio-technologies bring more chances to Bioinformatics and Biological
Engineering. Our paper introduces a way to solve the longest overlap region of
non-coding DNA sequences on using the Compute Unified Device Architecture
(CUDA) platform Intel(R) Core(TM) i3- 3110m quad-core. Compared to standard CPU
implementation, CUDA performance proves the method of the longest overlap
region recognition of noncoding DNA is an efficient approach to
high-performance bioinformatics applications. Studies show the fact that
efficiency of GPU performance is more than 20 times speedup than that of CPU
serial implementation. We believe our method gives a cost-efficient solution to
the bioinformatics community for solving longest overlap region recognition
problem and other related fields.
