PROBEmer: a web-based software tool for selecting optimal DNA oligos

被引：37

作者：

Emrich, SJ ^{[1
]}

Lowe, M

Delcher, AL

机构：

[1] Iowa State Univ, Interdept Bioinformat & Computat Biol, Ames, IA 50011 USA

[2] Loyola Coll Maryland, Dept Biol, Baltimore, MD USA

[3] Loyola Coll Maryland, Dept Phys, Baltimore, MD USA

[4] Loyola Coll Maryland, Dept Comp Sci, Baltimore, MD USA

[5] Inst Genom Res, Rockville, MD USA

来源：

NUCLEIC ACIDS RESEARCH | 2003年 / 31卷 / 13期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/nar/gkg569

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：3746 / 3750

页数：5

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