PROBEmer: a web-based software tool for selecting optimal DNA oligos
PROBEmer: a web-based software tool for selecting optimal DNA oligos
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DOI：
10.1093/nar/gkg569
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Delcher, AL
中科院分区：
文献类型：
--
作者：
Emrich, SJ;Lowe, M;Delcher, AL
PROBEmer（probemer.cs.loyola.edu）是一种基于网络的软件工具，它使研究人员能够为PCR应用和多重检测平台（包括寡核苷酸微阵列和基于珠的阵列）选择最佳寡核苷酸。给定两组核酸序列，靶组和非靶组，软件识别出在靶组成员中出现但不在非靶组中出现的寡核苷酸序列。为了帮助预测潜在的交叉杂交，PROBEmer计算非目标组中的所有近邻并显示它们的比对。该软件已用于获得基于16S rRNA基因的属特异性原核生物探针、用于表达分析的基因特异性探针和PCR引物。在本文中，我们描述了如何使用PROBEmer，它采用的计算方法，并通过这个软件工具确定的寡核苷酸的实验结果。
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.