БИОИНФОРМАЦИОННЫЙ АНАЛИЗ CRISPR/CAS СИСТЕМЫ ШТАММА YERSINIAPSEUDOTUBERCULOSIS IP32953
Аннотация и ключевые слова
Аннотация (русский):
Цель данного исследования: поиск и расшифровка CRISPR/Cas системы с помощью пакета программ в геноме Y.pseudotuberculosis IP32953. С помощью объединения результатов 4программных методов мы обнаружили в геноме штамма Y.pseudotuberculosis IP329353 один набор cas-генов и три локуса: YP1, YP2 и YP3. Через спейсеры кассет были обнаружены протоспейсеры в геномах: Y.pseudotuberculosis, Y.intermedia, Y.similis, Salmonella phage, Enterobacteria phage, и плазмиды Y.pseudotuberculosis IP32953 и Y.pseudotuberculosis IP31758.

Ключевые слова:
CRISPR/Cas, иерсинии, биоинформатика
Список литературы

1. AbbySS, NéronB, MénagerH, TouchonM, RochaEP(2014). MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PloS one, 9(10), e110726.

2. BiswasA, GagnonJN, BrounsSJ, FineranPC,BrownCM (2013). CRISPRTarget: bioinformatic predic-tion and analysis of crRNA targets. RNA biology, 10(5), 817-827.

3. BlandC, RamseyTL, SabreeF, LoweM, BrownK, KyrpidesNC, HugenholtzP (2007). CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC bioin-formatics, 8(1), 1.

4. EdgarRC (2007). PILER-CR: fast and accurate iden-tification of CRISPR repeats. BMC bioinformatics, 8(1), 1.

5. EppingerM, RosovitzMJ, FrickeWF, RaskoDA, KokorinaG, FayolleC, RavelJ (2007). The complete ge-nome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever. PLoS Genet, 3(8), e142

6. GajT, GersbachCA, BarbasCF (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397-405.

7. GasiunasG, SinkunasT, SiksnysV (2014). Molecu-lar mechanisms of CRISPR-mediated microbial immunity. Cellular and Molecular Life Sciences, 71(3), 449-465.

8. GrissaI, VergnaudG, PourcelC (2007). CRIS-PRFinder: a web tool to identify clustered regularly inter-spaced short palindromic repeats. Nucleic Acids Research, 35(2), W52-W57.

9. HammerlJA, FreytagB, LankaE, AppelB, HertwigS(2012). The pYV virulence plasmids of Yersinia pseudo-tuberculosis and Y.pestis contain a conserved DNA region responsible for the mobilization by the self-transmissible plasmid pYE854. Environmental Microbiology Reports, 4(4), 433-438.

10. JohnsonM, ZaretskayaI, RaytselisY, MerezhukY,McGinnisS, MaddenTL (2008). NCBI BLAST: a better web interface.Nucleic Acids Research, 36(2), W5-W9.

11. MakarovaKS, HaftDH, BarrangouR, BrounsSJ, CharpentierE, HorvathP, van der OostJ (2011). Evolution and classification of the CRISPR-Cas systems. Nature Re-views Microbiology, 9(6), 467-477.

12. OverbeekR, BegleyT, ButlerRM, ChoudhuriJV, ChuangHY, CohoonM, FonsteinM (2005). The subsys-tems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33(17), 5691-5702

13. PourcelC, SalvignolG, VergnaudG (2005). CRIS-PR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology, 151(3), 653-663

14. RousseauC, GonnetM., Le RomancerM., NicolasJ (2009). CRISPI: a CRISPR interactive database. Bioinfor-matics, 25(24), 3317-3318.

15. ZhouY, LiangY, LynchKH, DennisJJ, WishartDS (2011). PHAST: a fast phage search tool.Nucleic Acids Research, gkr485

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