A new Boolean logic algorithm for DNA sequence alignment

Abstract

Most of the DNA Sequence Alignment methods are mostly based on dynamic programming algorithms with low efficiency and poor accuracy. For these deficiencies, a new method is presented. This method is based on the Boolean logic and realized through FPGA. In the FPGA, First-In-First-Out Stack(FIFO) is used to save the DNA sequences, gate circuits (AND gates and OR gates) are used to realize DNA sequence alignment, and Finite Status Machine is used to control the whole process. The new method has been successfully designed and implemented. Its excellent merits are: “the gene mutation detection is immediately following the DNA sequences”. Experiment showed that, the new method can achieve fast and accurate alignment of the human DNA sequences. Specially, the alignment can be almost accomplished, as soon as the DNA sequences transmission comes to end.