Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus
Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus
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DOI：
10.1128/jcm.00135-06
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发表时间：
2006-08-01
影响因子：
9.4
通讯作者：
Rowlen, Kathy L.
中科院分区：
文献类型：
--
作者：
Mehlmann, Martin;Dawson, Erica D.;Rowlen, Kathy L.
DNA微阵列已被证明是基因表达分析的强大工具，并在诊断应用方面越来越有吸引力，例如用于病毒鉴定和亚型分析。选择适当的序列用于微阵列是一个挑战，特别是对于高度变异的生物，如流感病毒、人类免疫缺陷病毒和丙型肝炎病毒。这项工作的目标是开发一种有效的方法来挖掘大型数据库，以确定流感病毒基因组中的保守区域。从这些保守区中，选择了能够区分不同病毒类型和亚型的捕获和标记序列。该方法的突出特点是使用系统发育树进行数据简化，并选择数量相对较少的捕获和标记序列，能够识别广泛的流感病毒。所选序列的详细实验评估在配对论文中进行了描述。该软件可在通用公共许可证下免费获得，网址为http://www.colorado.edu/chemistry/RGHP/software/.
DNA microarrays have proven to be powerful tools for gene expression analyses and are becoming increasingly attractive for diagnostic applications, e.g., for virus identification and subtyping. The selection of appropriate sequences for use on a microarray poses a challenge, particularly for highly mutable organisms such as influenza viruses, human immunodeficiency viruses, and hepatitis C viruses. The goal of this work was to develop an efficient method for mining large databases in order to identify regions of conservation in the influenza virus genome. From these regions of conservation, capture and label sequences capable of discriminating between different viral types and subtypes were selected. The salient features of the method were the use of phylogenetic trees for data reduction and the selection of a relatively small number of capture and label sequences capable of identifying a broad spectrum of influenza viruses. A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at http://www.colorado.edu/chemistry/RGHP/software/.