Русская версия English version   
Том 17   Выпуск 2   Год 2022
Ахметзянова Л.У.1,2, Давлеткулов Т.М.1, Гарафутдинов Р.Р.3, Губайдуллин И.М.1,2

Применение алгоритма Ахо-Корасик для подбора праймеров для петлевой изотермической амплификации

Математическая биология и биоинформатика. 2022;17(2):250-265.

doi: 10.17537/2022.17.250.

Список литературы

  1. Mullis K., Faloona F. Specific synthesis of DNA in vitro via a polymerase catalyzed chain reaction. Meth. Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6
  2. Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985;230:1350–1354. doi: 10.1126/science.2999980
  3. Dietrich D., Uhl B., Sailer V., Holmes E.E., Jung M., Meller S., Kristiansen G. Improved PCR performance using template DNA from formalinfixed and paraffinembedded tissues by overcoming PCR inhibition. PLoS ONE. 2013;8. Article No. e77771. doi: 10.1371/journal.pone.0077771
  4. Notomi T., Okayam H., Masubuchi H., Yonekawa T., Watanabe K., Amino N., Hase T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research. 2000;28. Article No. e63. doi: 10.1093/nar/28.12.e63
  5. Garafutdinov R.R., Sakhabutdinova A.R., Gilvanov A.R., Chemeris A.V. Rolling circle amplification as a universal method for the analysis of a wide range of biological targets. Russian Journal of Bioorganic Chemistry. 2021;47(6):1172–1189. doi: 10.1134/S1068162021060078
  6. Garafutdinov R.R., Baymiev An.K., Maleev G.V., Alexeyev Ya.I., Zubov V.V., Chemeris D.A., Kiryanova O.Yu., Gubaydullin I.M., Matniyazov R.T., Sakhabutdinova A.R., Nikonorov Yu.M., Kuluev B.R., Baymiev Al.K., Chemeris A.V. Diversity of Pcr primers and principles of their design. Biomics. 2019;11(1):23–70. doi: 10.31301/2221-6197.bmcs.2019-04
  7. Mori Y., Notomi T. Loop-mediated isothermal amplification (LAMP): arapid, accurate, and cost-effective diagnostic method for infectious diseases. Chemother. 2009;15:62–69. doi: 10.1007/s10156-009-0669-9
  8. Chen S.H., Lin C.Y., Cho C.S., Lo C.Z., Hsiung C.A. Primer Design Assistant (PDA): A web-based primer design tool. Nucleic Acids Res. 2003;31:3751–3754. doi: 10.1093/nar/gkg560
  9. Nagamine K., Hase T., Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell Probes. 2002;16(3):223–229. doi: 10.1006/mcpr.2002.0415
  10. Eiken Chemical Co. http://loopamp.eiken.co.jp/e/lamp/anim.html (accessed 02 June 2020).
  11. New England Biolabs. https://international.neb.com/products/m1800-warmstart-colorimetric-lamp-2x-master-mix-dna-rna#Product%20Information (accessed 02 November 2022).
  12. Alhassan A., Li Z., Poole C., Carlow C. Expanding the MDx toolbox for filarial diagnosis and surveillance. Trends in Parasitology. 2015;31(8):391–400. doi: 10.1016/j.pt.2015.04.006
  13. Nkere C.K., Oyekanmi J.O., Silva G., Bömer M., Atiri G.I., Onyeka J., Maroya N.G., Seal S.E., Kumar P.L. Chromogenic Detection of Yam Mosaic Virus by Closed-Tube Reverse Transcription Loop-Mediated Isothermal Amplification (CT-RT-LAMP). Arch. Virol. 2018;163(14):1057–1061. doi: 10.1007/s00705-018-3706-0
  14. Wang C., Shen X., Lu J., Zhang L. Development of a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) System for Rapid Detection of HDV Genotype 1. Lett Appl. Microbiol. 2013;56(3):229–235. doi: 10.1111/lam.12039
  15. Makarova Yu.A., Zotikov A.A., Belyakova G.A., Alekseev B.Y., Shkurnikov M.Yu. Loop-mediated isothermal amplification: an effective method for express-diagnostics of cancer. Cancer Urology. 2018;14(2):88–99 (in Russ.). doi: 10.17650/1726-9776-2018-14-2-88-99
  16. Chemeris D.A., Kiryanova O.Yu., Gubaydullin I.M., Chemeris A.V. Design of primers for polymerase chain reaction (brief review of software and databases). Biomics. 2016;8(3):215–238 (in Russ.).
  17. Basic Local Alignment Search Tool. https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed 02 November 2022).
  18. Primer Explorer. http://primerexplorer.jp/e (accessed 02 November 2022).
  19. LAMP primer designing software. Primer Explorer. https://primerexplorer.jp/e/v4_manual/index.html (accessed 02 November 2022).
  20. LAMP Designer. Design Primers for Loop Mediated Isothermal Amplification. http://www.premierbiosoft.com/isothermal/lamp.html (accessed 02 November 2022).
  21. Kalendar R., Samuilova O., Ivanov K.I. 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics. 2017;109. Article No. 312319. doi: 10.1016/j.ygeno.2017.05.005
  22. Kalendar R., Tselykh T.V., Khassenov B., Ramanculov E.M. Introduction on using the FastPCR software and the related Java web tools for PCR and oligonucleotide assembly and analysis in PCR. Methods in Molecular Biology. 2017;1620:33–64. doi: 10.1007/978-1-4939-7060-5_2
  23. Restriction enzyme. https://dev.abcdef.wiki/wiki/Restriction_enzyme (accessed 02 November 2022).
  24. Kalendar R., Lee D., Schulman A. H. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics. 2011;98(2):137–144. doi: 10.1016/j.ygeno.2011.04.009
  25. GLAPD. https://github.com/jiqingxiaoxi/GLAPD (accessed 02 November 2022).
  26. Jia B., Li X., Liu W., Lu C., Lu X., Ma L., Li YY., Wei C. GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes. Front. Microbiol. 2019;10:1–9. doi: 10.3389/fmicb.2019.02860
  27. Maximato/lamprim. https://github.com/Maximato/lamprim (accessed 02 November 2022).
  28. Isothermal Amplification. https://lamp.neb.com/#!/ (accessed 02 November 2022).
  29. Loop Mediated Isothermal Amplification (LAMP) Tutorial. https://international.neb.com/tools-and-resources/video-library/loop-mediated-isothermal-amplification-lamp-tutorial  (accessed 02 November 2022).
  30. NEB LAMP Primer Design Tool. https://lamp.neb.com/#!/help (accessed 02 November 2022).
  31. Kiryanova O.Yu., Akhmetzianova L.U., Gubaydullin I.M. Search algorithms in the analysis of nucleotide sequences for unambiguous identification of genomes. Vestnik Bashkirskogo universiteta (Bulletin of Bashkir University). 2020;25(2):285–289.(in Russ.). doi: 10.33184/bulletin-bsu-2020.2.10
  32. RSDN Magazine. https://rsdn.org/article/alg/textsearch.xml (accessed 02 November 2022).
  33. Cormen T.H., Leiserson C.E., Rivest R.L., Stein C. Introduction to Algorithms. 3rd. MIT Press, 2009. ISBN 0-262-03384-4.
  34. Rabin-Karp Algorithm for Pattern Searching. https://www.geeksforgeeks.org/rabin-karp-algorithm-for-pattern-searching/ (accessed 02 November 2022).
  35. Akhmetzianova L.U., Davletkulov T.M., Garafutdinov R.R., Chemeris A.V., Gubaidullin I.M. Parallel Search Using an Algorithm Rabin–Karp for loop isothermal DNA amplification. In: Proceedings of the International Conference on Parallel computational technologies (PCT’2021). 2021. 278 p. (in Russ.) doi: 10.14529/pct2021
  36. Akhmetzianova L.U., Davletkulov T.M., Gubaidullin I.M., Islamgulov A.R. Parallel implementation of the primer search algorithm for loop-mediated isothermal amplification. Journal of Physics: Conference Series. 2021;2131(2). Paper 022004. doi: 10.1088/1742-6596/2131/2/022004
  37. Aho A.V., Corasick M.J. Efficient string matching: An aid to bibliographic search. Commun. ACM. 1975;18(6):333–340. doi: 10.1145/360825.360855
  38. Aho-Korasik algorithm. https://e-maxx.ru/algo/aho_corasick (accessed 02 November 2022).
  39. Aho-Korasik algorithm. https://neerc.ifmo.ru/wiki (accessed 02 November 2022).
  40. Fedorov D.Yu. Python High-Level Programming: Educational manual for applied bachelor's degree. Moscow, 2019. 161 p. (in Russ.).
  41. Biopython. https://biopython.org/ (accessed 02 November 2022).
  42. Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome. https://www.ncbi.nlm.nih.gov/nuccore/MN908947 (accessed 02 November 2022).
Содержание Оригинальная статья
Мат. биол. и биоинф.
2022;17(2):250-265
doi: 10.17537/2022.17.250
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
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