PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
| Autor: | Sangsu Bae, Omer Habib, Sung Ah Hong, Gue Ho Hwang, You Kyeong Jeong, Jin-Soo Kim, Kayeong Lim |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
Biology JavaScript Login computer.software_genre Prime (order theory) 03 medical and health sciences Upload 0302 clinical medicine Genetics CRISPR Web application Humans Guide RNA 030304 developmental biology computer.programming_language Gene Editing 0303 health sciences Internet business.industry Programming language High-Throughput Nucleotide Sequencing Web Server Issue Mutation Table (database) RNA CRISPR-Cas Systems business computer Sequence Alignment 030217 neurology & neurosurgery Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | Prime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3′ end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (>100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http://www.rgenome.net/pe-designer/ and http://www.rgenome.net/pe-analyzer/ without a login process. Graphical Abstract Graphical AbstractOverviews for input and output of PE-Designer and PE-Analyzer. |
| Databáze: | OpenAIRE |
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