Method and apparatus for performing similarity searching
    3.
    发明授权
    Method and apparatus for performing similarity searching 有权
    用于执行相似性搜索的方法和装置

    公开(公告)号:US08515682B2

    公开(公告)日:2013-08-20

    申请号:US13046395

    申请日:2011-03-11

    IPC分类号: G06F7/00

    摘要: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

    摘要翻译: 公开了一种用于执行相似性搜索的系统和方法。 这包括被配置为包括包括匹配级的流水线的可编程逻辑装置,所述匹配级被配置为接收包括多个数据串与查询串的多个子串之间的多个可能匹配的数据流。 流水线还可以包括位于匹配阶段下游的无间隙扩展预滤器级,预滤器级被配置为通过数据串与查询串的多个子串之间的模式匹配进行移位,并提供分数,使得只有模式匹配 超过用户定义的分数将从预过滤器阶段下游传递。 匹配阶段可以包括至少一个布隆过滤器。

    Method and Apparatus for Performing Similarity Searching
    8.
    发明申请
    Method and Apparatus for Performing Similarity Searching 有权
    用于执行相似性搜索的方法和装置

    公开(公告)号:US20110231446A1

    公开(公告)日:2011-09-22

    申请号:US13046395

    申请日:2011-03-11

    IPC分类号: G06F17/30

    摘要: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

    摘要翻译: 公开了一种用于执行相似性搜索的系统和方法。 这包括被配置为包括包括匹配级的流水线的可编程逻辑装置,所述匹配级被配置为接收包括多个数据串与查询串的多个子串之间的多个可能匹配的数据流。 流水线还可以包括位于匹配阶段下游的无间隙扩展预滤器级,预滤器级被配置为通过数据串与查询串的多个子串之间的模式匹配进行移位,并提供分数,使得只有模式匹配 超过用户定义的分数将从预过滤器阶段下游传递。 匹配阶段可以包括至少一个布隆过滤器。

    Method and apparatus for performing biosequence similarity searching
    9.
    发明申请
    Method and apparatus for performing biosequence similarity searching 有权
    用于执行生物相似性搜索的方法和装置

    公开(公告)号:US20070067108A1

    公开(公告)日:2007-03-22

    申请号:US11359285

    申请日:2006-02-22

    IPC分类号: G06F19/00

    摘要: A system and method for performing biological sequence similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of biological sequence data strings and a plurality of substrings of a query string. The pipeline may further include a ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the biological sequence data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

    摘要翻译: 公开了一种用于进行生物序列相似性搜索的系统和方法。 这包括被配置为包括包括匹配级的流水线的可编程逻辑设备,所述匹配级被配置为接收包括多个生物序列数据串与查询字符串的多个子串之间的多个可能匹配的数据流 。 流水线还可以包括位于匹配阶段下游的无间隙扩展预滤器级,预滤器级被配置为通过生物序列数据串与查询串的多个子串之间的模式匹配移位,并提供分数,使得只有模式 超过用户定义分数的匹配将从预过滤器阶段下游传递。 匹配阶段可以包括至少一个布隆过滤器。