期刊
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
卷 94, 期 2, 页码 152-160出版社
ELSEVIER IRELAND LTD
DOI: 10.1016/j.cmpb.2008.12.007
关键词
Primer design; DNA signature; DNA fingerprint; Solid-phase amplification; Multi-analyte assay; Diagnostics; HPV; Pathogen
类别
资金
- European Community
- European Regional Development Fund (ERDF)
Due to recent advances in genome sequencing, the detection of pathogens by DNA signatures, i.e. by oligonucleotide sequences that uniquely identify a specific genome, is becoming increasingly popular in modem clinical diagnostics. However, currently available screening methods, such as PCR and microarrays, lack multiplexing and sensitivity, respectively Solid-phase amplification (SPA) is an emerging approach with the potential to overcome these limitations. SPA-based diagnostic assays require both pathogen-specific and compatible primer pairs for many, often closely related pathogens. Currently, none of the available tools supports an automated design of such primer sets, making it an iterative, labor-intensive, and often difficult procedure. Here we describe hybseek, a web interface for efficient design of both pathogen-specific and compatible primer pairs for DNA-based diagnostic multi-analyte assays. hybseek achieves pathogen-specificity by selecting only candidates with unique 3' subsequence, and the degree of this uniqueness is quantitatively expressed by a specificity score. qPCR experimental data confirm the feasibility of our design strategy. The service is freely available at https://www.hybseek.com. (C) 2009 Elsevier Ireland Ltd. All rights reserved.
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