公开(公告)号：US20220415444A1

公开(公告)日：2022-12-29

申请号：US17850739

申请日：2022-06-27

Applicant: University of Washington

Inventor： Ling-Hong Hung ,  Ka Yee Yeung-Rhee

IPC: G16B30/10

Abstract: In some embodiments, a computer-implemented method of comparing strings representing nucleotide sequences is provided. A plurality of values representing Hamming distances between first strings and second strings are determined by converting value characters in the first string and the second string to a one hot encoding and converting any unknown characters in the first string and the second string to a zero value to create a first bit representation and a second bit representation; comparing the first bit representation and the second bit representation using a bitwise XOR operation to obtain a bitwise XOR result; counting a number of bits in the bitwise XOR result and multiplying the bitwise XOR result by two to obtain a bitcount result; and adjusting the bitcount result based on unknown characters in at least one of the first string and the second string to obtain the value representing the Hamming distance.

公开(公告)号：US20210089358A1

公开(公告)日：2021-03-25

申请号：US17018709

申请日：2020-09-11

Applicant: University of Washington

Inventor： Ka Yee Yeung-Rhee ,  Ling-Hong Hung ,  Wesley J. Lloyd

IPC: G06F9/50 ,  G06F9/455 ,  G06F21/64 ,  G16B25/10

Abstract: In some embodiments, novel approaches to processing bioinformatics data are used wherein the input data is divided into many small pieces that are processed in parallel by serverless functions. In effect, the functions can be used as on-demand compute units to form an affordable public-cloud version of a supercomputer. Some embodiments of the present disclosure can be used to accelerate the alignment of a single dataset. In some embodiments, the process of setting up the cloud infrastructure is automated so that the user need only to enter credentials from the cloud account. In some embodiments, these improvements are incorporated into an accessible and containerized graphical front-end that allows the user to use a browser to execute, monitor and modify all steps of the analyses from alignment to the display of the resulting differentially expressed genes.