LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures
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- 作者：Clinton Torres (1)
Elizabeth A Vitalis (1)
Brian R Baker (1)
Shea N Gardner (1)
Marisa W Torres (1)
John M Dzenitis (1) - 刊名：BMC Bioinformatics
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：12
- 期：1
- 全文大小：357KB
- 参考文献：1. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T: Loop-mediated isothermal amplification of DNA. / Nucleic Acids Research 2000, 28:E63-e63. 28(12) CrossRef
2. Hara-Kudo Y, Yoshino M, Kojima T, Ikedo M: Loop-mediated isothermal amplification for the rapid detection of Salmonella . / FEMS Microbiology Letters 2005, 253:155鈥?61. CrossRef
3. Mori Y, Kitao M, Tomita N, Notomi T: Real-time turbidimetry of LAMP reaction for quantifying template DNA. / Journal of Biochemical and Biophysical Methods 2004,59(2):145鈥?57. CrossRef
4. Nagamine K, Hase T, Notomi T: Accelerated reaction by loop-mediated isothermal amplification using loop primers. / Molecular and Cellular Probes 2002,16(3):223鈥?29. CrossRef
5. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. / Genome Res 2002,2(10):1611鈥?. CrossRef
6. Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. / Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365鈥?86.
7. Slezak T, Kuczmarski T, Ott L, Torres C, Medeiros D, Smith J, Truitt B, Mulakken N, Lam M, Vitalis E, Zemla A, Zhou CE, Gardner S: Comparative genomics tools applied to bioterrorism defense. / Briefings in Bioinformatics 2003,4(2):133鈥?49. CrossRef
8. SantaLucia J: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. / Proceedings of the National Academy of Sciences 1998, 95:1460鈥?465. CrossRef
9. Iwamoto T, Sonobe T, Hayashi K: Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium Tuberculosis Complex, M. avium , and M. intracellulare in Sputum Samples. / Journal of Clinical Microbiology 2003,41(6):2616鈥?622. CrossRef
10. Markham NR, Zuker M: DINAMelt web server for nucleic acid melting prediction. / Nucleic Acids Res 2005, 33:W577-W581. CrossRef
11. Poon L, Leung C, Tashiro M, Chan K, Wong B, Yuen K, Guan Y, Peiris J: Rapid Detection of the Severe Acute Respiratory Syndrome (SARS) Coronavirus by a Loop-Mediated Isothermal Amplification Assay. / Clinical Chemistry 2004,50(6):1050鈥?052. CrossRef
12. PrimerExplorer V4 from Eiken Chemical Co. Ltd [http://primerexplorer.jp/e/index.html] - 作者单位：Clinton Torres (1)
Elizabeth A Vitalis (1)
Brian R Baker (1)
Shea N Gardner (1)
Marisa W Torres (1)
John M Dzenitis (1)
1. Lawrence Livermore National Laboratory, Livermore, California, USA - ISSN：1471-2105
文摘
Background We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. Results LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures. The identified primers are conserved among target organism sequences. Primer combinations are optimized based on lengths, melting temperatures, and spacing among primer sites. We compare LAMP signature candidates for Staphylococcus aureus created both by LAVA and by PrimerExplorer. We also include signatures from a sample run targeting all strains of Mycobacterium tuberculosis. Conclusions We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/.