title: OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.
abstract: The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples. Here, we present Oligonucleotide Capture Probes for Pathogen Identification Database (OCaPPI-Db), an online capture probe database containing a set of 1,685 oligonucleotide probes allowing for the detection and identification of 30 biothreat agents up to the species level. This probe set can be used in its entirety as a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to the user's needs.
  
  
  
  : http://ocappidb.uca.works.
authors.affiliation: Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Gasc
authors.affiliation: Université d'Auvergne, IUT du Puy en Velay, Le Puy en Velay, France.
authors.forename: Antony
authors.initials: A
authors.lastname: Constantin
authors.affiliation: Université d'Auvergne, ISIT, Clermont-Ferrand, France.
authors.forename: Faouzi
authors.initials: F
authors.lastname: Jaziri
authors.affiliation: Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D054045:Biological Warfare Agents; D030561:Databases, Nucleic Acid; D015345:Oligonucleotide Probes / Q000235:genetics*; D013045:Species Specificity; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D054045:Biological Warfare Agents; D015345:Oligonucleotide Probes; D037521:Virulence Factors