Degenerate primer selection algorithms

2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology Pub Date : 2009-03-30 DOI:10.1109/CIBCB.2009.4925722

Dolly Sharma, Sudha Balla, S. Rajasekaran, Nikoletta DiGirolamo

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引用次数: 3

Abstract

The multiplex polymerase chain reaction (MP-PCR) is a quick and inexpensive technique in molecular biology for amplifying multiple DNA loci in a single Polymerase Chain Reaction (PCR). One of the criteria to achieve highly specific reaction products is to keep the concentration of the amplification primers low. In research, the dilemma associated with primer minimization for MP-PCR reactions has been formulated as the Multiple Degenerate Primer Selection Problem (MDPSP). MDPSP is related to the earlier Degenerate Primer Design (DPD) problem that has proven to be NP-complete. This paper formulates a new, so far, unexplored variant, the Multiple Degenerate Primer Selection Problem with Errors (MDPSPE) and introduces new algorithms for solving this new version. Furthermore, we implement an exact algorithm, DPS-HDR for solving the earlier MDPSP and compare the algorithm's performance on randomly generated data sets with DPS-HD, thus far the most efficient algorithm for solving MDPSP introduced in [2]. We expect to reduce the execution time of the algorithm in comparison to DPS-HD.1

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退化引物选择算法

多重聚合酶链式反应(MP-PCR)是一种快速、廉价的分子生物学技术，可在一次聚合酶链式反应(PCR)中扩增多个DNA位点。获得高特异性反应产物的标准之一是保持低浓度的扩增引物。在研究中，与MP-PCR反应的引物最小化相关的困境被表述为多重退化引物选择问题(MDPSP)。MDPSP与早期的退化引物设计(DPD)问题有关，该问题已被证明是np完全的。本文提出了一种新的，迄今为止尚未探索的变体，即带有错误的多重退化引物选择问题(MDPSPE)，并介绍了解决这个新版本的新算法。此外，我们实现了一种精确的算法DPS-HDR来求解早期的MDPSP，并将该算法在随机生成数据集上的性能与DPS-HD进行了比较，DPS-HD是迄今为止在[2]中引入的求解MDPSP的最有效算法。与DPS-HD.1相比，我们期望减少算法的执行时间

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2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology

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