Abstract
The results of this study include Yersinia pseudotuberculosis CRISPR/Cas system structure analysis. CRISPR/Cas system is a specific adaptive protection against heterogeneous genetic elements. The object of research was the complete genome of Y. pseudotuberculosis IP32953 (NC_006155). CRISPR/Cas system screening was performed by program modelling methods MacSyFinder ver. 1.0.2. CRISPR loci screening and analyzing were carried out by program package: CRISPR Recognition tool (CRT), CRISPI: a CRISPR Interactive database, CRISPRFinder, and PilerCR. Spacer sequences were used in order to find protospacers in ACLAME, GenBank-Phage and RefSeq-Plasmid databases by BLASTn search algorithm. Protospacer sequences could be found in genomes of phages, plasmids and bacteria. In last case complete genomes of bacteria were analyzed by online-tool PHAST: PHAge Search Tool. Y. pseudotuberculosis IP329353 has CRISPR/Cas system that consists of one sequence of cas-genes and three loci. These loci are far away from each other. Locus YP1 is situated in close proximity to cas-genes. Protospacers were found in genomes of Y. pseudotuberculosis PB1/+, Y. intermedia Y228, Y. similis str. 228, Salmonella phage, Enterobacteria phage, Y. pseudotuberculosis IP32953 plasmid pYV and plasmid of Y. pseudotuberculosis IP31758. Thus, the combination of four program methods allows finding CRISPR/Cas system more precisely. Spacer sequences could be used for protospacer screening.
Highlights
The results of this study include Yersinia pseudotuberculosis CRISPR/Cas system structure analysis
The object of research was the complete genome of Y. pseudotuberculosis IP32953 (NC_006155)
CRISPR/Cas system screening was performed by program modelling methods MacSyFinder ver. 1.0.2
Summary
В качестве объекта исследования использован геном штамма Y. pseudotuberculosis IP329353, представленный в базах данных GenBank (NC_006155). Для поиска CRISPR/Cas-систем применяли методы программного моделирования MacSyFinder Поиск точной гомологии последовательностей проводили при помощи установленных вспомогательных пакетов makeblastdb Поиск и расшифровку CRISPR-кассет производили при помощи 4 программных алгоритмов, включающих следующие программы: «PILER-CR: fast and accurate identification of CRISPR repeats», «CRISPI: a CRISPR Interactive database», «CRISPRFinder: CRISPRfinder program online» и «CRISPR Recognition Tool (CRT)» [3, 4, 8, 14]. Для скрининга фагов и плазмид по спейсерным сайтам было использовано онлайн-приложение «CRISPR Target: a tool to explore targets of CRISPRRNAs», фаговые и плазмидные базы данных ACLAME, GenBank и RefSeq и алгоритм поиска BLASTn [2, 10, 12]. Для поиска профагов использовали онлайн-приложение «PHAST: A Fast Phage Search Tool» [15]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
