Viral Sequence Identification in Metagenomes using Natural Language Processing Techniques

Abstract

Viral reads identification is one of the important steps in metagenomic data analysis. It shows up the diversity of the microbial communities and the functional characteristics of microorganisms. There are various tools that can identify viral reads in mixed metagenomic data using similarity and statistical tools. However, the lack of available genome diversity is a serious limitation to the existing techniques. In this work, we applied natural language processing approaches for document classification in analyzing metagenomic sequences. Text featurization is presented by treating DNA similar to natural language. These techniques reveal the importance of using the text feature extraction pipeline in sequence identification by transforming DNA base pairs into a set of characters with a term frequency and inverse document frequency techniques. Various machine learning classification algorithms are applied to viral identification tasks such as logistic regression and multi-layer perceptron. Moreover, we compared classical machine learning algorithms with VirFinder and VirNet, our deep attention model for viral reads identification on generated fragments of viruses and bacteria for benchmarking viral reads identification tools. Then, as a verification of our tool, It was applied to a simulated microbiome and virome data for tool verification and real metagenomic data of Roche 454 and Illumina for a case study.