SYSTEMS, DEVICES, AND METHODS OF A DATA PIPELINE

    公开(公告)号:US20240417752A1

    公开(公告)日:2024-12-19

    申请号:US18742805

    申请日:2024-06-13

    Abstract: Disclosed are data pipelines for string extraction, clustering, and comparison. A method may include extracting, from each plasmid genome sequence sequenced from genomes of plasmids, based on the presence of fixed flanking sequence markers (FFSMs) in the plasmid genome sequence, sequence regions. Each sequence region is within the FFSMs and includes a candidate inverted terminal repeat (ITR) sequence. The example method further includes clustering, based on perfect sequence identity, two or more sequence regions of the sequence regions to generate a clusters, merging, based on an alignment between their corresponding sequence regions, two or more clusters of the clusters; when a single cluster remains, identifying, based on a local alignment, a genotype of a candidate ITR sequence of the single cluster, and manufacturing, based on the genotype of the candidate ITR sequence, a plurality of AAV vectors using plasmids having ITR sequences with the genotype of the candidate ITR sequence.

    Methods and Compositions for Directed Genome Editing

    公开(公告)号:US20230076357A1

    公开(公告)日:2023-03-09

    申请号:US17735929

    申请日:2022-05-03

    Abstract: Provided herein are compositions and methods for increasing editing efficiency of a target nucleic acid. A composition may comprise a guide nucleic acid, a Cas9 nickase, or a reverse transcriptase. The reverse transcriptase may be fused to the Cas9 nickase. The reverse transcriptase may heterodimerize with the Cas9 nickase. The reverse transcriptase may bind to a guide nucleic acid. The reverse transcriptase may be engineered to increase processivity. The guide nucleic acid may be engineered to facilitate synthesis or editing of a sequence. The guide nucleic acid, Cas9 nickase, and reverse transcriptase may be engineered to fit within AAV vectors. The guide nucleic acid may comprise a region that binds to another region on the guide nucleic acid to improve gene editing.

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