Emrich Scott J, Lowe Mary, Delcher Arthur L
Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA.
Nucleic Acids Res. 2003 Jul 1;31(13):3746-50. doi: 10.1093/nar/gkg569.
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.
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。
