Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging.

ABSTRACT: DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a ribulose diphosphate carboxylase (rbcL) SNP barcoding (RSB) strategy using a decision tree algorithm. A

SUBMITTER: Yang CH 

PROVIDER: S-EPMC5846911 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature