Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction.
Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction.
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DOI：
10.5173/ceju.2016.654
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发表时间：
2016
影响因子：
1.2
通讯作者：
Ranjbar R
中科院分区：
文献类型：
--
作者：
Behzadi P;Najafi A;Behzadi E;Ranjbar R
尿路感染是主要疾病，可能由不同的病原微生物引起，特别是大肠杆菌。DNA芯片技术是一种准确、快速、灵敏、特异的诊断工具，可用于多种传染病的明确诊断和治疗。DNA微阵列是一种多工序技术，探针设计是其中的关键。因此，本研究的作者试图设计一系列有效和合适的长寡核苷酸微阵列探针，用于检测和鉴定不同菌株的致病性大肠杆菌，特别是尿路致病性大肠杆菌（UPEC）。以大肠杆菌O26 H11 11368 uid41021为标准菌株进行探针设计。该菌株在其他大肠杆菌致病性菌株中包含最大的核苷酸序列和最多的基因。为了在计算机上进行这项调查，使用NCBI数据库、GReview Server、PanSeq Server、Oligoanalyzer工具和AlleleID 7.7设计准确、合适、有效和灵活的长oligo微阵列探针。此外，还比较了大肠杆菌及其近缘微生物的基因组。本研究设计了15根长寡核苷酸微阵列探针，用于检测和鉴定不同的大肠杆菌菌株，如UPEC。这些探针具有最佳的物理化学特性。通过实用工具和软件对所设计探针的功能和结构特性进行了识别。采用可靠的先进技术和方法进行探针设计，保证了微阵列探针的高质量，使DNA微阵列技术更加灵活和有效的诊断技术。
Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of effective and proper long oligo microarray probes for detection and identification of different strains of pathogenic E.coli and in particular, uropathogenic E.coli (UPEC). E.coli O26 H11 11368 uid41021 was selected as the standard strain for probe designing. This strain encompasses the largest nucleotide sequence and the most number of genes among other pathogenic strains of E.coli. For performing this in silico survey, NCBI database, GReview Server, PanSeq Server, Oligoanalyzer tool, and AlleleID 7.7 were used to design accurate, appropriate, effective, and flexible long oligo microarray probes. Moreover, the genome of E.coli and its closely related microorganisms were compared. In this study, 15 long oligo microarray probes were designed for detecting and identifying different strains of E.coli such as UPEC. These probes possessed the best physico-chemical characteristics. The functional and structural properties of the designed probes were recognized by practical tools and softwares. The use of reliable advanced technologies and methodologies for probe designing guarentees the high quality of microarray probes and makes DNA microarray technology more flexible and an effective diagnostic technique.