公开(公告)号：US20200055903A1

公开(公告)日：2020-02-20

申请号：US16309645

申请日：2017-06-15

申请人： President and Fellows of Harvard College

发明人： Gleb Kuznetsov ,  Marc J. Lajoie ,  Matthieu M. Landon ,  Michael G. Napolitano ,  Daniel Bryan Goodman ,  Christopher J. Gregg ,  George M. Church ,  Nili Ostrov

IPC分类号： C07K14/245 ,  C12P21/00 ,  C12N15/10 ,  G16B20/50

摘要： Methods and systems for designing, testing, and validating genome designs are described herein. A computer-implemented method includes receiving data for a known genome and a list of alleles, identifying and removing occurrences of each allele in the known genome, determining a plurality of allele choices with which to replace occurrences in the known genome, generating a plurality of alternative gene sequences for a genome design based on the known genome, applying a plurality of rules or constraints or conditions or parameters or features to each alternative gene sequence by assigning a score for each rule or constraint or condition or parameter or feature in each alternative gene sequence, resulting in scores, scoring each alternative gene sequence based on a weighted combination of the scores, and selecting at least one alternative gene sequence as the genome design based on the scoring.

公开(公告)号：US11361845B2

公开(公告)日：2022-06-14

申请号：US16309645

申请日：2017-06-15

申请人： President and Fellows of Harvard College

发明人： Gleb Kuznetsov ,  Marc J. Lajoie ,  Matthieu M. Landon ,  Michael G. Napolitano ,  Daniel Bryan Goodman ,  Christopher J. Gregg ,  George M. Church ,  Nili Ostrov

IPC分类号： G16B35/10 ,  G16B20/50 ,  C07K14/245 ,  C12N15/10 ,  C12P21/00 ,  A61K38/00

摘要： Methods and systems for designing, testing, and validating genome designs based on rules or constraints or conditions or parameters or features and scoring are described herein. A computer-implemented method includes receiving data for a known genome and a list of alleles, identifying and removing occurrences of each allele in the known genome, determining a plurality of allele choices with which to replace occurrences in the known genome, generating a plurality of alternative gene sequences for a genome design based on the known genome, wherein each alternative gene sequence comprises a different allele choice, applying a plurality of rules or constraints or conditions or parameters or features to each alternative gene sequence by assigning a score for each rule or constraint or condition or parameter or feature in each alternative gene sequence, resulting in scores for the applied plurality of rules or constraints or conditions or parameters or features, scoring each alternative gene sequence based on a weighted combination of the scores for the plurality of rules or constraints or conditions or parameters or features, and selecting at least one alternative gene sequence as the genome design based on the scoring.

公开(公告)号：US20220246240A1

公开(公告)日：2022-08-04

申请号：US17719431

申请日：2022-04-13

申请人： President and Fellows of Harvard College

发明人： Gleb Kuznetsov ,  Marc J. Lajoie ,  Matthieu M. Landon ,  Michael G. Napolitano ,  Daniel Bryan Goodman ,  Christopher J. Gregg ,  George M. Church ,  Nili Ostrov

IPC分类号： G16B35/10 ,  G16B20/50 ,  C07K14/245 ,  C12N15/10 ,  C12P21/00

摘要： Methods and systems for designing, testing, and validating genome designs based on rules or constraints or conditions or parameters or features and scoring are described herein. A computer-implemented method includes receiving data for a known genome and a list of alleles, identifying and removing occurrences of each allele in the known genome, determining a plurality of allele choices with which to replace occurrences in the known genome, generating a plurality of alternative gene sequences for a genome design based on the known genome, wherein each alternative gene sequence comprises a different allele choice, applying a plurality of rules or constraints or conditions or parameters or features to each alternative gene sequence by assigning a score for each rule or constraint or condition or parameter or feature in each alternative gene sequence, resulting in scores for the applied plurality of rules or constraints or conditions or parameters or features, scoring each alternative gene sequence based on a weighted combination of the scores for the plurality of rules or constraints or conditions or parameters or features, and selecting at least one alternative gene sequence as the genome design based on the scoring.