元基因组分选问题:马尔可夫序列聚类

IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-28 DOI:10.1109/TMBMC.2023.3336254
Grant Greenberg;Ilan Shomorony
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引用次数: 0

摘要

元基因组学的目标是研究微生物群落的组成,通常采用高通量枪式测序法。在元基因组分选问题中,我们从混合基因组中观察随机子串(称为等位基因),并根据它们的起源基因组对它们进行聚类。根据经验观察,不同细菌物种的基因组可以根据它们的四核苷酸频率来区分,因此我们将这项任务建模为聚类由 ${M}$ 不同马尔可夫过程(其中 $M \ll N$ )产生的 ${N}$ 序列的问题。利用马尔可夫过程的大偏差原理,我们建立了完美分选的信息论极限。具体来说,我们证明等位基因的长度必须与两个最相似物种之间的切尔诺夫分歧率的倒数成比例。此外,我们的结果还暗示,应该用 KL 分歧率来衡量等位基因的距离,而不是实践中常用的欧氏距离。
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The Metagenomic Binning Problem: Clustering Markov Sequences
The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes and aim to cluster them according to their genome of origin. Based on the empirical observation that genomes of different bacterial species can be distinguished based on their tetranucleotide frequencies, we model this task as the problem of clustering ${N}$ sequences generated by ${M}$ distinct Markov processes, where $M \ll N$ . Utilizing the large-deviation principle for Markov processes, we establish the information-theoretic limit for perfect binning. Specifically, we show that the length of the contigs must scale with the inverse of the Chernoff divergence rate between the two most similar species. Furthermore, our result implies that contigs should be binned using the KL divergence rate as a measure of distance, as opposed to the Euclidean distance often used in practice.
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来源期刊
CiteScore
3.90
自引率
13.60%
发文量
23
期刊介绍: As a result of recent advances in MEMS/NEMS and systems biology, as well as the emergence of synthetic bacteria and lab/process-on-a-chip techniques, it is now possible to design chemical “circuits”, custom organisms, micro/nanoscale swarms of devices, and a host of other new systems. This success opens up a new frontier for interdisciplinary communications techniques using chemistry, biology, and other principles that have not been considered in the communications literature. The IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMSC) is devoted to the principles, design, and analysis of communication systems that use physics beyond classical electromagnetism. This includes molecular, quantum, and other physical, chemical and biological techniques; as well as new communication techniques at small scales or across multiple scales (e.g., nano to micro to macro; note that strictly nanoscale systems, 1-100 nm, are outside the scope of this journal). Original research articles on one or more of the following topics are within scope: mathematical modeling, information/communication and network theoretic analysis, standardization and industrial applications, and analytical or experimental studies on communication processes or networks in biology. Contributions on related topics may also be considered for publication. Contributions from researchers outside the IEEE’s typical audience are encouraged.
期刊最新文献
Table of Contents IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information Guest Editorial Introduction to the Special Feature on the 8th Workshop on Molecular Communications Guest Editorial Special Feature on Seeing Through the Crowd: Molecular Communication in Crowded and Multi-Cellular Environments IEEE Communications Society Information
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