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    Sequence information signal processor for local and global string comparisons
    3.
    发明授权
    Sequence information signal processor for local and global string comparisons 失效
    用于本地和全局字符串比较的序列信息信号处理器

    公开(公告)号：US5632041A

    公开(公告)日：1997-05-20

    申请号：US154633

    申请日：1993-11-18

    申请人： John C. Peterson ,  Edward T. Chow ,  Michael S. Waterman ,  Timothy J. Hunkapillar

    发明人： John C. Peterson ,  Edward T. Chow ,  Michael S. Waterman ,  Timothy J. Hunkapillar

    IPC分类号： G06F7/02 ,  G06F11/00 ,  G06F11/267 ,  G06F17/10 ,  G06F19/00

    CPC分类号： G06F11/2028 ,  G06F11/2051 ,  G06F17/10 ,  G06F7/02 ,  G06F11/2035 ,  G06F11/2043 ,  G06F11/2236 ,  G06F2201/83

    摘要： A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software.Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.

    摘要翻译： 一种序列信息信号处理集成电路芯片，被设计为基于Waterman和Smith定义的算法来执行动态规划算法的高速计算。 本发明的信号处理芯片被设计为线性收缩阵列的结构单元，通过将附加的序列信息信号处理芯片连接到阵列可以提高其性能。 该芯片提供了高速，低成本的线性阵列处理器，其可以定位高度相似的全局序列或其片段，例如来自两个不同DNA或蛋白质序列的连续子序列。 该芯片在优选实施例中使用CMOS VLSI技术来实现，以提供约40万个晶体管或100,000个门的等效物。 每个芯片提供16个处理元件，旨在提供16位，两次的补码操作，最大分数精度在-32,768和+32,767之间。 它旨在提供序列之间的比较，只要4,194,304个元素，无需外部软件，以及借助外部软件无限数量的元素序列之间。 每个序列可以分配不同的删除和插入重量函数。 每个处理器都具有独立变量的相似度测量装置。 因此，每个处理器可以使用不同的相似性度量来贡献最大值分数计算。

    Sequence information signal processor
    4.
    发明授权
    Sequence information signal processor 失效
    序列信息信号处理器

    公开(公告)号：US5964860A

    公开(公告)日：1999-10-12

    申请号：US831798

    申请日：1997-04-08

    申请人： John C. Peterson ,  Edward T. Chow ,  Michael S. Waterman ,  Timothy J. Hunkapillar

    发明人： John C. Peterson ,  Edward T. Chow ,  Michael S. Waterman ,  Timothy J. Hunkapillar

    IPC分类号： G06F7/02 ,  G06F11/00 ,  G06F11/267 ,  G06F17/10 ,  G06F19/00

    CPC分类号： G06F11/2028 ,  G06F11/2051 ,  G06F17/10 ,  G06F7/02 ,  G06F11/2035 ,  G06F11/2043 ,  G06F11/2236 ,  G06F2201/83

    摘要： An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

    摘要翻译： 电子电路用于比较诸如遗传序列的两个序列，以确定序列的哪个对齐产生最大的相似性。 该电路包括串联连接处理器的线性阵列，每个处理器存储来自一个序列的单个元件，并将该元素与另一个序列中的每个连续元素进行比较。 对于每个比较，处理器产生一个评分参数，该参数指示在那两个元素处结束的哪个段在序列之间产生最大程度的相似度。 处理器使用评分参数来生成相似的评分参数，用于比较存储的元素和来自其他序列的下一个连续元素之间的比较。 处理器还将得分参数提供给阵列中的下一个处理器，以用于为另一对元素生成类似的评分参数。 电子电路确定哪个处理器和序列的对齐产生具有最高值的评分参数。

    Oligoprobe designstation: a computerized method for designing optimal DNA probes
    5.
    发明授权
    Oligoprobe designstation: a computerized method for designing optimal DNA probes 失效
    Oligoprobe设计站：用于设计最佳DNA探针的计算机化方法

    公开(公告)号：US5556749A

    公开(公告)日：1996-09-17

    申请号：US975526

    申请日：1992-11-12

    申请人： Masato Mitsuhashi ,  Allan J. Cooper ,  Michael S. Waterman ,  Pavel A. Pevzner

    发明人： Masato Mitsuhashi ,  Allan J. Cooper ,  Michael S. Waterman ,  Pavel A. Pevzner

    IPC分类号： C12N15/00 ,  C12N15/10 ,  G06F17/30 ,  G06F17/50 ,  G06F19/20 ,  G06F19/22 ,  C12Q1/68 ,  G06F15/16 ,  G06F17/00

    CPC分类号： C12N15/10 ,  G06F19/20 ,  G06F19/22

    摘要： There is disclosed herein an invention which relates to the fields of genetic engineering, microbiology, and computer science, that allows a user, whether they be a molecular biologist or a clinical diagnostician, to calculate and design extremely specific oligonucleotide probes for DNA and mRNA hybridization procedures. The probes designed with this invention may be used for medical diagnostic kits, DNA identification, and potentially continuous monitoring of metabolic processes in human beings. The key features design oligonucleotide probes based on the GenBank database of DNA and mRNA sequences and examine candidate probes for specificity or commonality with respect to a user-selected experimental preparation. Two models are available: a Mismatch Model, that employs hashing and continuous seed filtration, and an H-Site Model, that analyzes candidate probes for their binding specificity relative to some known set of mRNA or DNA sequences. The preferred embodiment of this computerized design tool is written in the Borland.RTM. C++ language and runs under Microsoft.RTM. Windows.TM. on IBM.RTM. compatible personal computers.

    摘要翻译： 本文公开了一种涉及遗传工程，微生物学和计算机科学领域的发明，其允许用户（无论他们是分子生物学家还是临床诊断学家）计算和设计用于DNA和mRNA杂交的特异性寡核苷酸探针 程序。 用本发明设计的探针可用于医学诊断试剂盒，DNA鉴定和潜在的连续监测人类代谢过程。 关键是设计基于DNA和mRNA序列的GenBank数据库的寡核苷酸探针，并检查与用户选择的实验准备相关的特异性或共同性的候选探针。 有两种型号可供选择：使用散列和连续种子过滤的不匹配模型，以及H-Site模型，它们可以相对于一些已知的一组mRNA或DNA序列分析其结合特异性的候选探针。 该计算机化设计工具的优选实施例是用Borland TM C ++语言编写的，并且在IBM TM兼容个人计算机上的Microsoft TM Windows TM下运行。