公开(公告)号：US20210317523A1

公开(公告)日：2021-10-14

申请号：US17355823

申请日：2021-06-23

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Yu LI ,  Sheng WANG ,  Renmin HAN

IPC: C12Q1/6869 ,  G16B40/30 ,  G16B40/10 ,  G16B30/20 ,  G06N3/08

Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.

公开(公告)号：US20200370110A1

公开(公告)日：2020-11-26

申请号：US16769127

申请日：2018-10-30

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Yu LI ,  Sheng WANG ,  Renmin HAN

IPC: C12Q1/6869 ,  G16B40/10 ,  G16B30/20 ,  G16B40/30

Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.

公开(公告)号：US20200035325A1

公开(公告)日：2020-01-30

申请号：US16432123

申请日：2019-06-05

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Renmin HAN ,  Sheng WANG ,  Yu LI

IPC: G16B30/00

Abstract: A method for global mapping between a first sequence Xp and a second sequence Xg. The method includes receiving the first sequence Xp and the second sequence Xg at a computing device, wherein the first sequence Xp is related to measured raw electrical current signals and the second sequence Xg is related to calculated electrical current signals; applying a continuous wavelet transform (CWT) algorithm to each of the first and second sequences Xp and Xg to obtain raw CWT signals and expected CWT signals, respectively; extracting raw features and expected features from the raw CWT signals and the expected CWT signals, respectively; generating a context-dependent boundary Bi around a previous warping path WI, wherein the previous warping path WI is calculated using a dynamic time warping (DTW) algorithm that relates the raw features to the expected features and I is an index associated with an element of the previous warping path; calculating a new warping path WI−1 based on the context-dependent boundary BI; and identifying a nucleotide sequence associated with the first sequence Xp and the second sequence Xg, based on the new warping path WI−1.

公开(公告)号：US20210350876A1

公开(公告)日：2021-11-11

申请号：US17285255

申请日：2019-10-16

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Sheng WANG ,  Renmin HAN

IPC: G16B40/10 ,  G16B30/10 ,  G06K9/62 ,  G01N33/487

Abstract: A method for similarity searching directly on nanopore raw current signals, the method including receiving a reference genome sequence; receiving a query genome sequence; transforming the reference genome sequence, with a nanopore sequencing device, into a raw current signal X; transforming the query genome sequence, based on a pore model, into a query current signal Y; and mapping the query current signal Y to the raw current signal X based on a subsequence extension of dynamic time warping distance Dist, which calculates a distance between the raw current signal X and a padded signal query Y′. The padded signal query Y′ is the query current signal Y to which an element y0 has been added, the raw current signal X and the query current signal Y are electrical currents, and the raw current signal X corresponds to a genome of an organism.