Abstract:
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/.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Torres C,Vitalis EA,Baker BR,Gardner SN,Torres MW,Dzenitis JMdoi
10.1186/1471-2105-12-240subject
Has Abstractpub_date
2011-06-16 00:00:00pages
240issn
1471-2105pii
1471-2105-12-240journal_volume
12pub_type
杂志文章abstract:BACKGROUND:Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics...
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pub_type: 杂志文章
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更新日期:2005-01-01 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2008-05-28 00:00:00
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更新日期:2011-01-11 00:00:00
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更新日期:2011-08-25 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2018-11-30 00:00:00
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