Search International and National Patent Collections

1. (WO2018089223) REDUCED MEMORY NUCLEOTIDE SEQUENCE COMPARISON

Pub. No.:    WO/2018/089223    International Application No.:    PCT/US2017/059141
Publication Date: Fri May 18 01:59:59 CEST 2018 International Filing Date: Wed Nov 01 00:59:59 CET 2017
IPC: G06F 19/22
Applicants: MICROSOFT TECHNOLOGY LICENSING, LLC
Inventors: LO, Daniel
CHUNG, Eric
OVTCHAROV, Kalin
PANDYA, Ravindra
HECKERMAN, David
SNYTSAR, Roman
Title: REDUCED MEMORY NUCLEOTIDE SEQUENCE COMPARISON
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.