title: hybseek: pathogen primer design tool for diagnostic multi-analyte assays.
abstract: 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 modern 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.
authors.affiliation: University of Applied Sciences, Softwarepark 11, 4232 Hagenberg, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Frech
authors.forename: Karin
authors.initials: K
authors.lastname: Breuer
authors.forename: Bernhard
authors.initials: B
authors.lastname: Ronacher
authors.forename: Thomas
authors.initials: T
authors.lastname: Kern
authors.forename: Christof
authors.initials: C
authors.lastname: Sohn
authors.forename: Gerhard
authors.initials: G
authors.lastname: Gebauer
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D030541:Databases, Genetic; D016678:Genome; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D027383:Papillomaviridae / Q000235:genetics / Q000472:pathogenicity; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers