基于布尔逻辑的双序列比对协处理器的设计与实现  

Design and Implementation of a Coprocessor which Completes Pairwise Sequence Alignment with a New Algorithm Based on Boolean Logic

作　　者：王进科[1] 冯萍[1] 康继昌[1] 陈亚东[1] 

机构地区：[1]西北工业大学计算机学院,陕西西安710072

出　　处：《西北工业大学学报》2011年第1期1-5,共5页Journal of Northwestern Polytechnical University

摘　　要：文章针对基因研究中的快速完成双序列比对工作的需要,设计了一种双序列比对协处理器。该协处理器通过USB接口与主机进行通信,采用基于布尔逻辑的比对算法完成双序列的比对。对碱基进行优化编码,使得用简单的门电路实现比对规则;使用流水寄存器,使得读碱基和序列比对并行工作,从而快速地完成具有显著相似性的DNA序列的比对。实验表明该协处理器具有结构简单、高效稳定、升级方便等特点。Aim. The introduction of the full paper points out that, to our knowledge, the existing algorithms for pairwise sequence alignment are traditional. Sections 1,2 and 3 give full explanation of the subject matter meant by the title. We emphasize in particular that our coprocessor and new algorithm are, we believe, very effective for pairwise sequence alignment of long sequence whose similarity is marked. The experimental results in section 4 con- firm preliminarily what we have just emphasized. The core of sections 1, 2 and 3 consists of： （ 1 ） the coprocessor designed by us in FPGA （Field Programmable Gate Array） communicates with the host via USB interface; （2） we simplify the ASCII 8bit-codes of a base into 4bit-codes; （3） our new algorithm can he implemented with simple gate circuits; （4） we adopt two sets of 3-stage pipeline registers; in this way, pairwise sequence alignment and base-pair reading work in parallel, so our coprocessor can quickly complete pairwise sequence alignment.

关 键 词：双序列比对 协处理器 布尔逻辑 算法 

分 类 号：TP399[自动化与计算机技术—计算机应用技术]