Abstract:
:Loop-mediated isothermal amplification (LAMP) technology has been applied in a wide range of fields such as detection of foodborne bacteria and clinical pathogens due to its simplicity and efficiency. However, existing LAMP primer designing systems require a conserved gene or a short genome region as input, and they can't design group-specific primers. With the growing number of whole genomes available, it is possible to design better primers to target a set of genomes with high specificity based on whole genomes. We present here a whole Genome based LAMP primer designer (GLAPD), a new system to design LAMP primer for a set of target genomes using whole genomes. Candidate single primer regions are identified genome wide and then combined into LAMP primer sets. For a given set of target genomes, only primer sets amplifying them and only these genomes will be output. In order to accelerate the primer designing, a GPU version is provided as well. The effectiveness of primers designed by GLAPD has been assessed for a wide range of foodborne bacteria. GLAPD can be accessed at http://cgm.sjtu.edu.cn/GLAPD/ or https://github.com/jiqingxiaoxi/GLAPD.git. A simple online version is also supplied to help users to learn and test GLAPD: http://cgm.sjtu.edu.cn/GLAPD/online/.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Jia B,Li X,Liu W,Lu C,Lu X,Ma L,Li YY,Wei Cdoi
10.3389/fmicb.2019.02860subject
Has Abstractpub_date
2019-12-13 00:00:00pages
2860issn
1664-302Xjournal_volume
10pub_type
杂志文章abstract::Comparative studies have shown that diet, life history, and phylogeny interact to determine microbial community structure across mammalian hosts. However, these studies are often confounded by numerous factors. Selection experiments offer unique opportunities to validate conclusions and test hypotheses generated by co...
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journal_title:Frontiers in microbiology
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journal_title:Frontiers in microbiology
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doi:10.3389/fmicb.2012.00139
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journal_title:Frontiers in microbiology
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pub_type: 杂志文章,评审
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pub_type: 杂志文章
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journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.00422
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journal_title:Frontiers in microbiology
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doi:10.3389/fmicb.2019.02804
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journal_title:Frontiers in microbiology
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doi:10.3389/fmicb.2016.01351
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doi:10.3389/fmicb.2017.00924
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journal_title:Frontiers in microbiology
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doi:10.3389/fmicb.2016.01590
更新日期:2016-10-04 00:00:00
abstract::Exposure to environmental toxins such as heavy metals can perturb the development and stability of microbial communities associated with human or animal hosts. Widespread arsenic contamination in rivers and riparian habitats therefore presents environmental and health concerns for populations living near sources of co...
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doi:10.3389/fmicb.2018.01323
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pub_type: 杂志文章
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journal_title:Frontiers in microbiology
pub_type: 杂志文章
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pub_type: 杂志文章,评审
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pub_type: 杂志文章
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更新日期:2017-06-30 00:00:00
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pub_type: 杂志文章
doi:10.3389/fmicb.2017.00184
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