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A systolic array for sequence comparison based on two-logic-levels processing element

机译：基于双逻辑级处理元素的序列比较的收缩阵列

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In this work, we implement a dynamic programming (DP) algorithm for sequence comparison (SC) purposes. We aimed at obtaining a better compromise between the processing acceleration optimization and the hardware cost. A simplified edit distance (ED) calculation formula is used, where we introduce two new simplified logical equations based on this last formula. A systolic array (SA) based on our simplified processing element (PE) can compare sequences with a great length and a high processing frequency. Our system speed-up shows a gain varying between 13% and 142% compared to other systems, according to the considered FPGA family.

机译：在这项工作中，我们实现了一种动态编程（DP）算法，用于序列比较（SC）目的。我们旨在在加工加速度优化和硬件成本之间获得更好的折衷。使用简化的编辑距离（ED）计算公式，其中我们基于此最后公式介绍了两个新的简化逻辑方程。基于我们的简化处理元件（PE）的收缩阵列（SA）可以比较具有较大长度和高处理频率的序列。根据所考虑的FPGA家族，我们的系统加速显示与其他系统相比的增益不同于13％和142％。

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《Institute of Electrical and Electronics Engineers Northeast Workshop on Circuits and Systems 》|2007年||共4页
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dynamic programming; field programmable gate arrays; systolic arrays; FPGA; dynamic programming algorithm; edit distance calculation formula; sequence comparison; systolic array; two-logic-levels processing element; Parallel Hardware Acceleration;

机译：动态编程;现场可编程门阵列;收缩阵列;FPGA;动态编程算法;编辑距离计算公式;序列比较;收缩阵列;两个逻辑级处理元素;并行硬件加速;

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1. Multi-functional systolic array with reconfigurable micro-power processing elements [J] . E.I. Milovanovic, T.R. Nikolic, M.K. Stojcev, Microelectronics reliability . 2009 ,第7期

机译：具有可重新配置的微功率处理元件的多功能脉动阵列
2. Determiningthe Number of Processing Elements in Systolic Arrays [J] . I.?. Milovanovi?, M.K. Stoj?ev, T.I. Toki?E.I. Milovanovi? Facta Universitatis. Series Mathematics and Informatics . 2000 ,第2000期

机译：确定脉动阵列中的处理元件数
3. Synthesis and Implementation of 3D IIR Filter As a Processing Element of Systolic Array Architecture [J] . Shantha Selva Kumari R, Vishnu Priya M International Journal of Innovative Research in Science, Engineering and Technology . 2014 ,第3期

机译：3D IIR滤波器作为脉动阵列结构处理元件的综合与实现
4. A Systolic Array for Sequence Comparison based on Two-Logic-Levels Processing Element [C] . Nasreddine Hireche, J. M. Pierre Langlois, Gabriela Nicolescu IEEE North-East Workshop on Circuits and Systems . 2007

机译：基于双逻辑级处理元素的序列比较的收缩阵列
5. Field-programmable gate array implementation of a scalable integral image architecture based on systolic arrays. [D] . De la Cruz, Juan A. 2011

机译：基于脉动阵列的可扩展积分图像体系结构的现场可编程门阵列实现。
6. Comparison of RNA Expression Profiles Based on Maize Expressed Sequence Tag Frequency Analysis and Micro-Array Hybridization [O] . John Fernandes, Volker Brendel, Xiaowu Gai, 2002

机译：基于玉米表达序列标签频率分析和微阵列杂交的RNA表达谱比较
7. Figure 4: (A) One conserved sequence, which occurs 79 times in 46,264 binding site peaks from the ChIP-seq data-set. The mutation profile of this conserved sequence is illustrated, where ’_ ’ indicates this base is unchanged; DEL indicates this base is lost; INS X indicates a new base X is inserted in front of this base. (B) Several repeated elements patterns are listed. (C) In the first column, the top five DNA motifs, mined by meme-chip tools (Machanick Bailey, 2011) are illustrated. The resemblant conserved sequences, found by the CFSP algorithm are listed in the second column. In the third column, the position-specific scoring matrices, which are transformed from mutational information are listed. The similarity between meme motif and resemblant conserved sequence with PSSM format was calculated via a stamp motif comparison tool (Mahony Benos, 2007). The E-values for the similarity of those pairs is displayed in the fourth column. (D) One motif is selected in each group clustered by gkmsvm descriptors, and the corresponding motif found by the CFSP algorithm is listed below. (E) There are additional datasets (File No: ENCFF100GRL, ENCFF616IRT, ENCFF870CER, Target: SREBF1) collected from https://www.encodeproject.org. The top two motifs are selected in each file using meme tools, and the corresponding motifs found by our algorithm are listed below. [O] . -1

机译：图4：（a）一种保守序列，其发生在芯片-SEQ数据集中的46,264个结合位点峰值中的79倍。说明了这种保守序列的突变分布，其中'_'表示该碱度不变; del表示此基础丢失; INS X表示新的基础X插入此基础前面。（b）列出了几种重复的元素模式。（c）在第一栏中，示出了由MEME芯片工具（Machanick＆Bailey，2011）开采的前五个DNA主题。由CFSP算法发现的相应保守序列列于第二列中。在第三列中，列出了从突变信息转换的特定位置的评分矩阵。 MEME主题与PSSM格式的相似性与PSSM格式之间的相似性通过邮票图章比较工具（Mahony＆Benos，2007）计算。这些对相似性的电子值显示在第四列中。（d）在由GKMSVM描述符聚集的每个组中选择了一个图案，下面列出了CFSP算法的相应主题。（e）从https://www.encodeproject.org收集的，有附加数据集（文件no：cernff100grl，cenf616irl，conf8.20cer，target：srebf1）。使用MEME工具在每个文件中选择前两个图案，并且我们的算法发现的相应主题如下所示。

A systolic array for sequence comparison based on two-logic-levels processing element

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