Fast DNA Barcode Generating Algorithm Using Radix Coding Method
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High multiplexing of samples is critical for next generation sequencing (NGS) where within one lane 10s or 100s of samples can be sequenced simultaneously. Often the limited factor is the number of unique DNA sequences that can be used as molecular tags, i.e. barcodes. We propose the creation of a new algorithm to generate these sequences for sample barcoding. Devising algorithms that make the designing possible in a reasonable run-time and high quality output has been always challenging. In this paper we introduce a new search method which utilizes proposed coding of features named Radix Coding. This method facilitates searching between multi-feature objects where all the features need to be considered in the search process. This method can also be generalized and applied to similar applications and outperforms common and time consuming search algorithms as it reduces the run-time by a significant factor. © 2012 IEEE.
author list (cited authors)
Nikooienejad, A., Metz, R., Yoon, B., & Johnson, C. D.