Rapid Identification and Quantification of Organisms from Heterogeneous DNA

描述（由申请人提供）：本提案的具体目标是创建一种快速识别高通量DNA测序数据中存在的生物体物种组成的方法。主要假设是，每个生物体都有一个独特的k-mer频率向量，可以从生物体的基因组中构建该频率向量，从而使用线性代数和统计学方法快速识别异质DNA测序样品中的生物体。本研究的目标是建立一个用于存储和操作k-mer频率向量的计算框架，开发一个用于从异质短读DNA测序样本中识别生物体并估计其丰度的回归模型，并将该方法应用于纽约市范围内的病原体检测，作为纽约市“PathoMap”项目的一部分。

DESCRIPTION (provided by applicant): The specific objective of this proposal is to create a method for quickly identifying the species composition of organisms present in high-throughput DNA sequencing data. The main hypothesis is that every organism has a unique k-mer frequency vector that can be constructed from the organism's genome to quickly identify the organism in heterogeneous DNA sequencing samples using methods from linear algebra and statistics. The goals of this research are to build a computational framework for storing and manipulating k-mer frequency vectors, develop a regression model for identifying organisms and estimating their abundance from heterogeneous, short-read DNA sequencing samples, and apply this method for city-wide pathogen detection as part of the New York City "PathoMap" project.