论文标题

PWM2VEC:冠状病毒峰序列病毒宿主规范的有效嵌入方法

PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences

论文作者

Ali, Sarwan, Bello, Babatunde, Chourasia, Prakash, Punathil, Ria Thazhe, Zhou, Yijing, Patterson, Murray

论文摘要

COVID-19大流行,仍然是未知的,是一个重要的开放问题。有人猜测蝙蝠是可能的起源。同样,有许多密切相关的(电晕)病毒,例如SARS,发现通过Civets传播。对不同宿主的研究可能是对人类致命病毒的潜在载体和发射器的研究,对于理解,缓解和预防当前和未来的大流行者至关重要。在冠状病毒中,表面蛋白或尖峰蛋白是确定宿主特异性的重要组成部分,因为它是病毒与宿主细胞膜之间的接触点。在本文中,我们将超过五千个冠状病毒的宿主从其尖峰蛋白序列分类为宿主,将它们隔离为鸟类,蝙蝠,骆驼,骆驼,猪,人类和羊毛的不同宿主的簇,仅举几例。我们提出了一个基于众所周知的位置权威矩阵(PWM)的特征嵌入,我们称之为PWM2VEC,并用于从这些冠状病毒的尖峰蛋白序列中生成特征向量。虽然我们的嵌入受到PWM在生物应用中的成功启发,例如确定蛋白质功能或识别转录因子结合位点,但我们是(就我们所知的最好的)而言,我们是在病毒序列中使用PWM的第一个(据我们所知),以生成固定长度的特征矢量表示。现实世界数据的结果表明,在使用PWM2VEC时,与基线模型相比,我们能够表现出色。我们还使用信息增益来测量不同氨基酸的重要性,以显示氨基酸,这对于预测给定冠状病毒的宿主很重要。

COVID-19 pandemic, is still unknown and is an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona-) viruses, such as SARS, which was found to be transmitted through civets. The study of the different hosts which can be potential carriers and transmitters of deadly viruses to humans is crucial to understanding, mitigating and preventing current and future pandemics. In coronaviruses, the surface (S) protein, or spike protein, is an important part of determining host specificity since it is the point of contact between the virus and the host cell membrane. In this paper, we classify the hosts of over five thousand coronaviruses from their spike protein sequences, segregating them into clusters of distinct hosts among avians, bats, camels, swines, humans and weasels, to name a few. We propose a feature embedding based on the well-known position-weight matrix (PWM), which we call PWM2Vec, and use to generate feature vectors from the spike protein sequences of these coronaviruses. While our embedding is inspired by the success of PWMs in biological applications such as determining protein function, or identifying transcription factor binding sites, we are the first (to the best of our knowledge) to use PWMs in the context of host classification from viral sequences to generate a fixed-length feature vector representation. The results on the real world data show that in using PWM2Vec, we are able to perform comparably well as compared to baseline models. We also measure the importance of different amino acids using information gain to show the amino acids which are important for predicting the host of a given coronavirus.

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