DNABarcodes: an R package for the systematic construction of DNA sample tags
DNABarcodes: an R package for the systematic construction of DNA sample tags
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DOI：
10.1093/bioinformatics/btw759
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发表时间：
2017-03-15
期刊：
影响因子：
5.8
通讯作者：
Buschmann, Tilo
中科院分区：
文献类型：
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作者：
Buschmann, Tilo
动机：DNA条形码通常用于分子和细胞生物学中的计数和区分目的。并不是每一组DNA序列都同样适合这个目标。人们对更复杂的条形码设计的需求日益增长，而可用的工具却很少。我们准备了一个R软件包，它结合了已知的算法和创新的方法，用于高效，灵活和接近最佳的生成鲁棒的条形码sets.Results：我们的R软件包'DNABarcodes'从几个基本的输入参数（例如：G.长度、距离度量、最小距离、化学性质）。它满足了条形码从头设计中大多数特定实验需求的细节。此外，该软件包允许分析现有的DNA条形码集以及生成这些现有集合的子集，以改善其纠错和检测特性。'DNABarcodes'是为速度，多功能性，可证明的正确性和大集合大小而设计的。
Motivation: DNA barcodes are commonly used for counting and discriminating purposes in molecular and cell biology. Not every set of DNA sequences is equally suitable for this goal. There is a growing demand for more sophisticated barcode designs, with only few tools available. We prepared an R package that combines known algorithms and innovative methods for the efficient, flexible and near-optimal generation of robust barcode sets.Results: Our R-software package 'DNABarcodes' generates sets of DNA barcodes from a few basic input parameters (e. g. length, distance metric, minimum distance, chemical properties). It satisfies the specifics of most particular experimental demands in de novo design of barcodes. Additionally, the package allows analysing existing sets of DNA barcodes as well as the generation of subsets of those existing sets to improve their error correction and detection properties. 'DNABarcodes' was designed for speed, versatility, provable correctness and large set sizes.