OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
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DOI：
10.1093/nar/gkg580
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Kauppinen, S
中科院分区：
文献类型：
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作者：
Tolstrup, N;Nielsen, PS;Kauppinen, S
我们报告的新软件，OligoDesign，它提供了最佳的设计LNA（锁核酸）取代的寡核苷酸的功能基因组学应用的发展。LNA构成一类新型的双环RNA类似物，其对它们的互补DNA和RNA靶分子具有异常高的亲和力和特异性。OligoDesign软件的特点是通过全基因组BLAST分析识别和过滤靶序列，以最大限度地减少与非靶序列的交叉杂交。此外，它还包括预测LNA取代的寡核苷酸的解链温度、自退火和二级结构以及预测靶核苷酸序列的二级结构的程序。针对查询基因中的每个可能的LNA寡核苷酸计算所有这些性质的个体得分，并且OligoDesign程序根据组合的模糊逻辑得分对LNA捕获探针进行排名，并且最终在输出中将最高得分的探针返回给用户。我们已经成功地使用OligoDesign工具来设计秀丽隐杆线虫LNA寡核苷酸微阵列，其允许监测一组120个潜在标记基因的表达，用于各种应激和毒理学过程以及毒理学相关途径。OligoDesign程序可在http://lnatools.com/上免费访问。
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/.