OCaPPI-Db：一个通过杂交捕获进行病原体鉴定的寡核苷酸探针数据库。

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.

作者信息

Gasc Cyrielle, Constantin Antony, Jaziri Faouzi, Peyret Pierre

机构信息

Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France.

Université d'Auvergne, IUT du Puy en Velay, Le Puy en Velay, France.

出版信息

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/baw172.

DOI:10.1093/database/baw172

PMID:28365722

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5467545/

Abstract

UNLABELLED

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.

DATABASE URL

: http://ocappidb.uca.works.

摘要

未标注

检测和鉴定涉及生物和农业恐怖主义行为的细菌病原体对于避免病原体在环境中扩散以及在人群中传播至关重要。传统的分子方法，如聚合酶链反应（PCR）扩增、DNA微阵列或鸟枪法测序，在评估环境样本时存在各种局限性，可能导致结果不准确。我们开发了一种杂交捕获策略，该策略使用一组寡核苷酸探针来靶向和富集环境样本中感兴趣的生物标志物。在此，我们展示了用于病原体鉴定数据库的寡核苷酸捕获探针（OCaPPI-Db），这是一个在线捕获探针数据库，包含一组1685个寡核苷酸探针，可用于检测和鉴定多达物种水平的30种生物威胁因子。该探针集既可以作为一个全面的诊断工具整体使用，也可以根据用户需求限制为针对特定病原体或毒力因子的一组探针。