PROBEmer：一种用于选择最佳DNA寡核苷酸的基于网络的软件工具。
PROBEmer: A web-based software tool for selecting optimal DNA oligos.
作者信息
Emrich Scott J, Lowe Mary, Delcher Arthur L
机构信息
Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA.
出版信息
Nucleic Acids Res. 2003 Jul 1;31(13):3746-50. doi: 10.1093/nar/gkg569.
Abstract
PROBEmer (http://probemer.cs.loyola.edu) is a web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. The software has been used to obtain genus-specific prokaryotic probes based on the 16S rRNA gene, gene-specific probes for expression analyses and PCR primers. In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool.
摘要
PROBEmer（http://probemer.cs.loyola.edu）是一款基于网络的软件工具，它能让研究人员为PCR应用以及包括寡核苷酸微阵列和基于微珠的阵列在内的多重检测平台选择最佳的寡核苷酸。给定两组核酸序列，即目标组和非目标组，该软件会识别出在目标组成员中出现但不在非目标组中出现的寡核苷酸序列。为了帮助预测潜在的交叉杂交情况，PROBEmer会计算非目标组中的所有近邻，并展示它们的比对结果。该软件已被用于基于16S rRNA基因获得属特异性原核生物探针、用于表达分析的基因特异性探针以及PCR引物。在本文中，我们描述了如何使用PROBEmer、它所采用的计算方法以及通过该软件工具识别出的寡核苷酸的实验结果。
相似文献
1
PROBEmer: A web-based software tool for selecting optimal DNA oligos.PROBEmer：一种用于选择最佳DNA寡核苷酸的基于网络的软件工具。
Nucleic Acids Res. 2003 Jul 1;31(13):3746-50. doi: 10.1093/nar/gkg569.
2
A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization.一种用于酿酒酵母的全基因组微阵列探针的新颖设计，可最大限度地减少交叉杂交。
BMC Genomics. 2003 Sep 22;4(1):38. doi: 10.1186/1471-2164-4-38.
3
Oligo Design: a computer program for development of probes for oligonucleotide microarrays.寡核苷酸设计：一种用于开发寡核苷酸微阵列探针的计算机程序。
Biotechniques. 2003 Dec;35(6):1216-21. doi: 10.2144/03356bc02.
4
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.PRIMEGENS：用于微阵列分析的基因特异性探针的强大且高效的设计
Bioinformatics. 2002 Nov;18(11):1432-7. doi: 10.1093/bioinformatics/18.11.1432.
5
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling.寡核苷酸设计：用于基因表达谱分析的锁核酸（LNA）寡核苷酸捕获探针的优化设计。
Nucleic Acids Res. 2003 Jul 1;31(13):3758-62. doi: 10.1093/nar/gkg580.
6
Design of long oligonucleotide probes for functional gene detection in a microbial community.用于微生物群落中功能基因检测的长寡核苷酸探针设计
Bioinformatics. 2005 Nov 15;21(22):4092-100. doi: 10.1093/bioinformatics/bti673. Epub 2005 Sep 13.
7
Selection of optimal DNA oligos for gene expression arrays.用于基因表达阵列的最佳DNA寡核苷酸的选择。
Bioinformatics. 2001 Nov;17(11):1067-76. doi: 10.1093/bioinformatics/17.11.1067.
8
A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.一种用于设计全基因组寡核苷酸阵列的通用方法，已在金黄色葡萄球菌的基因分型、缺失图谱绘制和基因表达分析中得到验证。
BMC Genomics. 2005 Jun 17;6:95. doi: 10.1186/1471-2164-6-95.
9
Mprobe 2.0: computer-aided probe design for oligonucleotide microarray.Mprobe 2.0：用于寡核苷酸微阵列的计算机辅助探针设计
Appl Bioinformatics. 2006;5(3):181-6. doi: 10.2165/00822942-200605030-00006.
10
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA.使用16S核糖体DNA进行有效探针自动设计的综合比对序列构建（CASCADE-P）
Bioinformatics. 2003 Aug 12;19(12):1461-8. doi: 10.1093/bioinformatics/btg200.
引用本文的文献
1
BOND: Basic OligoNucleotide Design.邦德：基本寡核苷酸设计。
BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.
2
Universal fingerprinting chip server.通用指纹识别芯片服务器。
Bioinformation. 2012;8(12):586-8. doi: 10.6026/97320630008586. Epub 2012 Jun 28.
3
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.人类肠道芯片的开发与应用：对年轻和老年成年人丰富微生物群中普遍存在的分类群的分析。
Environ Microbiol. 2009 Jul;11(7):1736-51. doi: 10.1111/j.1462-2920.2009.01900.x. Epub 2009 Mar 11.
4
ESTPiper--a web-based analysis pipeline for expressed sequence tags.ESTPiper——一个用于表达序列标签的基于网络的分析流程。
BMC Genomics. 2009 Apr 21;10:174. doi: 10.1186/1471-2164-10-174.
5
PrimerHunter: a primer design tool for PCR-based virus subtype identification.引物猎手：一种用于基于PCR的病毒亚型鉴定的引物设计工具。
Nucleic Acids Res. 2009 May;37(8):2483-92. doi: 10.1093/nar/gkp073. Epub 2009 Mar 5.
6
An evaluation of custom microarray applications: the oligonucleotide design challenge.定制微阵列应用的评估：寡核苷酸设计挑战
Nucleic Acids Res. 2009 Apr;37(6):1726-39. doi: 10.1093/nar/gkp053. Epub 2009 Feb 10.
7
A Java-based tool for the design of classification microarrays.一种用于设计分类微阵列的基于Java的工具。
BMC Bioinformatics. 2008 Aug 4;9:328. doi: 10.1186/1471-2105-9-328.
8
Primique: automatic design of specific PCR primers for each sequence in a family.Primique：为一个家族中的每个序列自动设计特异性PCR引物。
BMC Bioinformatics. 2007 Oct 3;8:369. doi: 10.1186/1471-2105-8-369.
9
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.格林SCPrimer：一种用于从多序列比对中设计简并引物的快速综合工具。
Nucleic Acids Res. 2006;34(22):6605-11. doi: 10.1093/nar/gkl966. Epub 2006 Nov 28.
10
Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions.通过优化杂交条件提高 DNA 微阵列定量的重现性和准确性。
BMC Bioinformatics. 2006 Sep 6;7 Suppl 2(Suppl 2):S17. doi: 10.1186/1471-2105-7-S2-S17.
本文引用的文献
1
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.PRIMEGENS：用于微阵列分析的基因特异性探针的强大且高效的设计
Bioinformatics. 2002 Nov;18(11):1432-7. doi: 10.1093/bioinformatics/18.11.1432.
2
Fast algorithms for large-scale genome alignment and comparison.用于大规模基因组比对和比较的快速算法。
Nucleic Acids Res. 2002 Jun 1;30(11):2478-83. doi: 10.1093/nar/30.11.2478.
3
Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays.通过在cDNA阵列上选择非冗余靶标来避免交叉杂交。
Bioinformatics. 2002 Feb;18(2):321-2. doi: 10.1093/bioinformatics/18.2.321.
4
Quantitation of DNA sequences in environmental PCR products by a multiplexed, bead-based method.采用基于磁珠的多重方法对环境PCR产物中的DNA序列进行定量分析。
Appl Environ Microbiol. 2002 Feb;68(2):1010-3. doi: 10.1128/AEM.68.2.1010-1013.2002.
5
GenBank.基因银行
Nucleic Acids Res. 2002 Jan 1;30(1):17-20. doi: 10.1093/nar/30.1.17.
6
Selection of optimal DNA oligos for gene expression arrays.用于基因表达阵列的最佳DNA寡核苷酸的选择。
Bioinformatics. 2001 Nov;17(11):1067-76. doi: 10.1093/bioinformatics/17.11.1067.
7
The RDP-II (Ribosomal Database Project).核糖体数据库项目II（RDP-II）
Nucleic Acids Res. 2001 Jan 1;29(1):173-4. doi: 10.1093/nar/29.1.173.
8
The Comprehensive Microbial Resource.综合微生物资源
Nucleic Acids Res. 2001 Jan 1;29(1):123-5. doi: 10.1093/nar/29.1.123.
9
Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria.用于检测硫酸盐还原菌系统发育亚群的寡核苷酸探针和PCR引物的开发。
Microbiology (Reading). 2000 Jul;146 ( Pt 7):1693-1705. doi: 10.1099/00221287-146-7-1693.
10
Enrichment of Geobacter Species in Response to Stimulation of Fe(III) Reduction in Sandy Aquifer Sediments.砂质含水层沉积物中因Fe(III)还原刺激导致的地杆菌属物种富集
Microb Ecol. 2000 Feb;39(2):153-167. doi: 10.1007/s002480000018.
Zotero 插件