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鉴定高通量DNA测序数据中存在的微生物物种组成的方法。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构建，以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计算框架，用于存储和操作k-mer频率向量，开发一个回归模型，用于识别生物体和估计其丰度从异质性，短读段DNA测序样品，并应用这种方法进行全市范围的病原体检测的一部分，纽约市“PathoMap”项目。

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.