IP Reservoir, LLC

Washington University

IP Resevoir, LLC

Joseph Marion Lancaster

Roger Dean Chamberlain

Kevin Brian Sprague

Michael John Henrichs

Terry Tidwell

Mark Allen Franklin

Jason R White

Kwame Gyang

Praveen Krishnamurthy

Arpith Chacko Jacob

Jeremy Daniel Buhler

Louis Kelly Thomas

Alex St John

Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a structured format such as a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.

Method and apparatus for accelerated format translation of data in a delimited data format

Improved computer technology is disclosed for enabling high performance stream processing on data such as complex, hierarchical data. In an example embodiment, a dynamic field schema specifies a dynamic field format for expressing the incoming data. An incoming data stream is then translated according to the dynamic field schema into an outgoing data stream in the dynamic field format. Stream processing, including field-specific stream processing, can then be performed on the outgoing data stream.

Dynamic field data translation to support high performance stream data processing

Apparatuses and methods are disclosed for comparing a first biosequence string with a second biosequence string to assess similarity between those biosequence strings. For example, a field programmable gate array (FPGA) can be used to (1) detect substrings of the second biosequence string that are matches to substrings of the first biosequence string, and (2) map the detected substrings of the second biosequence string to corresponding positions in the first biosequence string where the detected substrings are located based on a data structure that links substrings of the first biosequence string to positions in the first biosequence string where the substrings of the first biosequence string are located. These operations can be used to seed an alignment between the first and second biosequence strings that permits comparisons to be performed over longer substrings of the first and second biosequence strings so that similarities between those longer substrings can be quantified.

Method and apparatus for performing similarity searching

Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a mapped variable field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.

Various methods and apparatuses are described for performing high speed translations of data. In an example embodiment, record layout detection can be performed for data. In another example embodiment, data pivoting prior to field-specific data processing can be performed.

Method and apparatus for accelerated record layout detection

Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.

A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units. Further, a hash table may be generated to map a set of strings to keys. In other examples, the hash table may be used to map a set of substrings to a position in a larger string.

Method and apparatus for accelerated data translation using record layout detection

A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units.

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.

An apparatus and method for performing similarity searching on a data stream with respect to a query string are disclosed, where the data stream comprises a plurality of data substrings, and where the query string comprises a plurality of query substrings. A programmable logic device is used to filter the data stream to find a plurality of possible matches between the data substrings and a plurality of the query substrings, wherein the data substrings and the query substrings comprise a plurality of characters. From these possible matches, a determination can be made as to a similarity between the query string and at least a portion of the data stream.

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St. Louis, MO, United States of America

Joseph Marion Lancaster