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公开(公告)号：US20180137085A1
公开(公告)日：2018-05-17
申请号：US15351372
申请日：2016-11-14
Applicant: Microsoft Technology Licensing, LLC
Inventor： Daniel Lo , Eric Chung , Kalin Ovtcharov , Ravindra Pandya , David Heckerman , Roman Snytsar
IPC: G06F17/16
Abstract: Comparisons between two nucleotide sequences can be performed by customized integrated circuity that can implement a Smith Waterman analysis in a reduced memory footprint, storing and referencing only individual portions, or subsections, of a two-dimensional matrix that is representative of the comparison between the two nucleotide sequences. As the backtracking proceeds, backtracking metadata corresponding to a cell from a subsection that is not currently retained in memory can be required. Such a subsection can be regenerated from previously generated scores associated with checkpoint cells of the two-dimensional matrix that comprise two edges of the subsection being regenerated. Moreover, to further reduce memory consumption, the backtracking metadata stored for each cell can comprise four binary digits: two indicative of a directional assignment, one indicative of whether the corresponding cell is part of a deletion stretching across multiple contiguous cells, and one analogously indicative of insertions stretching across multiple contiguous cells.
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公开(公告)号：US20180137237A1
公开(公告)日：2018-05-17
申请号：US15349725
申请日：2016-11-11
Applicant: Microsoft Technology Licensing, LLC
Inventor： Daniel Lo , Eric Chung , Kalin Ovtcharov , Ravindra Pandya , David Heckerman
Abstract: Comparisons between two nucleotide sequences can be performed by customized integrated circuitry that can implement a Smith Waterman analysis in series, as opposed to the parallel implementations known in the art. Series performance enables such customized integrated circuitry to take advantage of optimizations, including enveloping thresholds that demarcate between cells of a two-dimensional matrix for which nucleotide comparisons are to be performed, and cells of the two-dimensional matrix for which no such comparison need be performed, and, instead, a value of zero can simply be entered. Additionally, such customized integrated circuitry facilitates the combination of multiple control units, each directing the comparison of a unique pair of nucleotides, with a single calculation engine that can generate values for individual cells of the two-dimensional matrices by which such pairs of nucleotides are compared.
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公开(公告)号：US10566076B2
公开(公告)日：2020-02-18
申请号：US15349725
申请日：2016-11-11
Applicant: Microsoft Technology Licensing, LLC
Inventor： Daniel Lo , Eric Chung , Kalin Ovtcharov , Ravindra Pandya , David Heckerman
Abstract: Comparisons between two nucleotide sequences can be performed by customized integrated circuitry that can implement a Smith Waterman analysis in series, as opposed to the parallel implementations known in the art. Series performance enables such customized integrated circuitry to take advantage of optimizations, including enveloping thresholds that demarcate between cells of a two-dimensional matrix for which nucleotide comparisons are to be performed, and cells of the two-dimensional matrix for which no such comparison need be performed, and, instead, a value of zero can simply be entered. Additionally, such customized integrated circuitry facilitates the combination of multiple control units, each directing the comparison of a unique pair of nucleotides, with a single calculation engine that can generate values for individual cells of the two-dimensional matrices by which such pairs of nucleotides are compared.
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公开(公告)号：US10241970B2
公开(公告)日：2019-03-26
申请号：US15351372
申请日：2016-11-14
Applicant: Microsoft Technology Licensing, LLC
Inventor： Daniel Lo , Eric Chung , Kalin Ovtcharov , Ravindra Pandya , David Heckerman , Roman Snytsar
Abstract: Comparisons between two nucleotide sequences can be performed by customized integrated circuitry that can implement a Smith Waterman analysis in a reduced memory footprint, storing and referencing only individual portions, or subsections, of a two-dimensional matrix that is representative of the comparison between the two nucleotide sequences. As the backtracking proceeds, backtracking metadata corresponding to a cell from a subsection that is not currently retained in memory can be required. Such a subsection can be regenerated from previously generated scores associated with checkpoint cells of the two-dimensional matrix that comprise two edges of the subsection being regenerated. Moreover, to further reduce memory consumption, the backtracking metadata stored for each cell can comprise four binary digits: two indicative of a directional assignment, one indicative of whether the corresponding cell is part of a deletion stretching across multiple contiguous cells, and one analogously indicative of insertions stretching across multiple contiguous cells.
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