共查询到16条相似文献,搜索用时 171 毫秒
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细小病毒B19诊断芯片的初步研究 总被引:1,自引:0,他引:1
初步探讨并制备细小病毒B19诊断芯片,进行实验室验证.用基因芯片点样仪将细小病毒B19诊断探针固定在特殊处理的玻片上,以细小病毒B19质粒重复检测.运用限制性显示(RD)技术,用Cy5标记的通用引物进行荧光标记,通过与基因芯片杂交,严谨洗涤,将非特异性的标记片段洗脱后,经扫描仪扫描,计算机解读.杂交结果显示,Cy5标记的探针均出现杂交信号,而阴性对照和空白对照的杂交信号均很弱:芯片检测具有高特异性、敏感性和可重复性.初步建立了较可靠的制备与检测细小病毒B19诊断芯片的方法,经验证诊断准确率高,假阳性率低. 相似文献
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探讨研制能同时检测HBV、HCV、HIV、HAV、GBV-C/HGV和B19的微阵列监控芯片。根据病毒公开发表序列,序列比对,得出保守区域,设计病毒的特异性检测探针,同时设置阴性、阳性参照探针,制备监控微阵列。利用随机引物PCR方法标记样品中的病毒靶序列,标记产物与微阵列上的探针杂交,清洗、扫描后进行结果分析。通过对质粒或模式分子的检测以及经HBV、HCV、HIV临床标本的验证,发现该微阵列监控芯片具有良好的特异性。其对质粒的检测灵敏度可达102病毒拷贝数,对临床标本的检测灵敏度可达103病毒拷贝数。此外,该微阵列监控芯片可检测出病毒混合感染血清。为微阵列监控芯片应用于此六种血液病毒的检测打下一定的基础。 相似文献
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伊蚊浓核病毒三维结构的比较分析 总被引:1,自引:0,他引:1
细小病毒是目前已知的结构最小的病毒, 其宿主范围很广. 利用冷冻电镜和三维重构技术获得了伊蚊浓核病毒1.2 nm分辨率下的三维结构, 并利用计算机生物信息处理技术和氨基酸序列比对技术比较了该病毒和其他细小病毒的结构和序列的异同. 尽管均属于浓核病毒亚科, 但是无论从衣壳结构还是其蛋白质的氨基酸序列上, 伊蚊浓核病毒和其他昆虫的细小病毒都有很大差异. 相比之下, 伊蚊浓核病毒和人类B19细小病毒的衣壳蛋白相似性较大, 两者的结构蛋白和非结构蛋白一致性也高于伊蚊浓核病毒与其他昆虫的细小病毒的一致性. 此结果表明: 伊蚊浓核病毒和人类B19细小病毒有着密切关系, 前者可能来源于B19病毒的较近期变种. 相似文献
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研制和优化寡核苷酸芯片以初步实现对多种常见HPV(Human papillomavirus)病毒的分型检测.应用生物学软件对四型常见HPV病毒(6、11、16、18型)的全基因组序列进行分析,设计具有型特异性、熔解温度(Tm)相近的~60 mer寡核苷酸探针,对玻片片基进行优化处理后,点样制备成寡核苷酸基因芯片.将含HPV全长基因序列的质粒作为阳性标准品,利用梯度限制性荧光标记技术对其进行荧光标记,标记好的样品与芯片杂交.结果显示HPV样品与相应的型特异性探针杂交有明显的荧光信号,而与阴性对照探针和空白对照探针没有杂交信号.通过对芯片片基处理和样品荧光标记方法的优化,可以提高芯片检测的杂交特异性和荧光信号强度. 相似文献
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YODA: selecting signature oligonucleotides 总被引:3,自引:0,他引:3
Nordberg EK 《Bioinformatics (Oxford, England)》2005,21(8):1365-1370
MOTIVATION: Selecting oligonucleotide probes for use in microarray design, and other applications requiring signature sequences, involves identifying sequences which will bind strongly to their intended target, while binding only weakly (or preferably, not at all) to non-target sequences which may be present in the hybridization reaction. While many tools to assist in selection of such sequences exist, all the ones we examined lack important oligo design and software features. RESULTS: YODA is an application for assisting biological researchers in selecting signature sequences. It incorporates a custom sequence similarity search to find potential cross-hybridizing non-target sequences. For this task, most oligo design tools rely on BLAST, which is ill suited for it due to an unacceptable risk of false negatives. YODA supports multiple probe design goals including single-genome, multiple-genome, pathogen-host and species/strain-identification. A graphical interface is provided as well as a command-line interface, both of which support many user-controlled parameters. YODA is easy to install and use and runs on Windows, Mac OS X and Linux platforms. AVAILABILITY: Freely available (LGLP) along with source code and additional documentation at http://pathport.vbi.vt.edu/YODA CONTACT: enordber@vbi.vt.edu. 相似文献
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SNPbox: a modular software package for large-scale primer design 总被引:1,自引:0,他引:1
Weckx S De Rijk P Van Broeckhoven C Del-Favero J 《Bioinformatics (Oxford, England)》2005,21(3):385-387
SUMMARY: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions. AVAILABILITY: The software is available from the authors upon request. SUPPLEMENTARY INFORMATION: SNPbox_supplement. 相似文献
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小鼠细胞因子相关基因表达检测寡核苷酸芯片的制备及分析 总被引:12,自引:0,他引:12
生物芯片技术用于基因表达谱研究是近年来发展起来的一项新技术 ,该方法本质上是基于对一玻璃片或膜表面上固定的cDNA或寡核苷酸的分子杂交 ,这一新技术可同时测定成千上万个基因的作用方式 ,几周获得的信息用其它方法可能要几年才能得到 ,是以定量方式同时监测大量基因相对表达的强有力的新方法[1 ,2 ] 。国内外目前主要采用cDNA芯片进行基因表达的检测 ,芯片制备所用的DNA探针一般为已知基因cDNA克隆的PCR扩增产物或EST的扩增产物[3~ 8] 。对基因的表达检测来说 ,cDNA芯片技术是一条非常适用的检测方法 ,但在有… 相似文献
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目的:建立一种质量控制芯片来监测样品标记、杂交和检测过程中的失误。方法:针对GFP基因设计的4条60mer寡核苷酸探针和1条阳性对照探针polv(U)与流感寡核苷酸探针一起打印在DAKO玻片上,并构建了GFP基因的克隆载体和体外表达载体,将从这两种重组载体上获得的绿色荧光蛋白(Green Fluorescent Protein,GFP)基因的ILNA、DNA片段和人的全血样品中的DNA用限制性显示技术(Restriction Display technology,RD)扩增标记,将标记的样品和荧光标记的通用引物U分别与芯片杂交、检测,并对扫描的结果进行统计分析。结果:GFP探针与相应的样品杂交时出现阳性信号,阳性对照探针在所有的杂交中均出现阳性信号,而空白对照则未检测荧光信号。结论:建立的质控芯片具有较好的敏感性和特异性,可以用于基因芯片中的质量监控。 相似文献
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Tolstrup N Nielsen PS Kolberg JG Frankel AM Vissing H Kauppinen S 《Nucleic acids research》2003,31(13):3758-3762
We report the development of new software, OligoDesign, which provides optimal design of LNA (locked nucleic acid) substituted oligonucleotides for functional genomics applications. LNAs constitute a novel class of bicyclic RNA analogs having an exceptionally high affinity and specificity toward their complementary DNA and RNA target molecules. The OligoDesign software features recognition and filtering of the target sequence by genome-wide BLAST analysis in order to minimize cross-hybridization with non-target sequences. Furthermore it includes routines for prediction of melting temperature, self-annealing and secondary structure for LNA substituted oligonucleotides, as well as secondary structure prediction of the target nucleotide sequence. Individual scores for all these properties are calculated for each possible LNA oligonucleotide in the query gene and the OligoDesign program ranks the LNA capture probes according to a combined fuzzy logic score and finally returns the top scoring probes to the user in the output. We have successfully used the OligoDesign tool to design a Caenorhabditis elegans LNA oligonucleotide microarray, which allows monitoring of the expression of a set of 120 potential marker genes for a variety of stress and toxicological processes and toxicologically relevant pathways. The OligoDesign program is freely accessible at http://lnatools.com/. 相似文献
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An application of a quantitative PCR-based method was developed for the detection of human parvovirus B19 DNA. The procedure was characterised according to guidelines for the validation of analytical procedures. Furthermore, the reliability was demonstrated by the correct quantitation of samples of an international collaborative study. This application might be useful for studies focussed on removal and/or inactivation procedures of human parvovirus B19 as well as for general screening purposes of biological materials. 相似文献