Extraction of CRISPR-targeted sequences from the metagenome.
STAR Protoc
; 3(3): 101525, 2022 09 16.
Article
em En
| MEDLINE
| ID: mdl-35780428
ABSTRACT
Homology-based search is commonly used to uncover mobile genetic elements (MGEs) from metagenomes, but it heavily relies on reference genomes in the database. Here we introduce a protocol to extract CRISPR-targeted sequences from the assembled human gut metagenomic sequences without using a reference database. We describe the assembling of metagenome contigs, the extraction of CRISPR direct repeats and spacers, the discovery of protospacers, and the extraction of protospacer-enriched regions using the graph-based approach. This protocol could extract numerous characterized/uncharacterized MGEs. For complete details on the use and execution of this protocol, please refer to Sugimoto et al. (2021).
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Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Metagenoma
/
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas
Limite:
Humans
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article