Efficient primer design algorithms
Efficient primer design algorithms
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DOI：
10.1093/bioinformatics/17.3.214
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发表时间：
2001-03-01
期刊：
影响因子：
5.8
通讯作者：
Mecklenburg, M
中科院分区：
文献类型：
--
作者：
Kämpke, T;Kieninger, M;Mecklenburg, M
动机：引物设计涉及各种参数，例如基于字符串的比对分数、解链温度、引物长度和GC含量。这需要一个多标准决策的设计方法。一些标准的值是很容易计算，而其他需要激烈的calculation.Results：参考点的方法被认为是易于权衡的偏离理想值的所有标准。一些准则计算是基于动态程序的值迭代，其运行时间可以由一个低次多项式的限制。对于设计标准的PCR引物，该方案提供了一个相对增益的计算速度高达50：1的ad-hoc计算方法。单PCR引物对已被用作模型系统，以简化计算加速因子的量化。该程序的结构是为了便于分析大量的引物对与微小的修改。该方案显著提高了引物设计通量，从而促进了寡核苷酸在广泛应用中的使用，包括：多重PCR和其他基于核酸的扩增系统，以及邮政编码靶向，寡核苷酸微阵列和基于核酸的纳米工程。可用性：DOPRIMER软件的公共版本可在http://doprimer.interactiva.de上访问。
Motivation: Primer design involves various parameters such as string-based alignment scores, melting temperature, primer length and GC content. This entails a design approach from multicriteria decision making. Values of some of the criteria are easy to compute while others require intense calculations.Results: The reference point method was found to be tractable for trading-off between deviations from ideal Values of all the criteria. Some criteria computations are based on dynamic programs with value iteration whose run time can be bounded by a low-degree polynomial. For designing standard PCR primers, the scheme offers in a relative gain in computing speed of up to 50:1 over ad-hoc computational methods. Single PCR primer pairs have been used as model systems in order to simplify the quantization of the computational acceleration factors. The program has been structured so as to facilitate the analysis of large numbers of primer pairs with minor modifications. The scheme significantly increases primer design throughput which in turn facilitates the use of oligonucleotides in a wide range of applications including: multiplex PCR and other nucleic acid-based amplification systems, as well as in zip code targeting, oligonucleotide microarrays and nucleic acid-based nanoengineering.Availability: A public version of the software DOPRIMER is accessible under http://doprimer.interactiva.de.