Background: In recent years, DNA barcoding has become an important tool for biologists to identify species and understand their natural biodiversity. The complexity of barcode data makes it difficult to analyze quickly and effectively. Manual classification of this data cannot keep up to the rate of increase of available data.
Results: In this study, we propose a new method for DNA barcode classification based on the distribution of nucleotides within the sequence. By adding the covariance of nucleotides to the original natural vector, this augmented 18-dimensional natural vector makes good use of the available information in the DNA sequence. The accurate classification results we obtained demonstrate that this new 18-dimensional natural vector method, together with the random forest classifier algorthm, can serve as a computationally efficient identification tool for DNA barcodes. We performed phylogenetic analysis on the genus Megacollybia to validate our method. We also studied how effective our method was in determining the genetic distance within and between species in our barcoding dataset.
Conclusions: The classification performs well on the fungi barcode dataset with high and robust accuracy. The reasonable phylogenetic trees we obtained further validate our methods. This method is alignment-free and does not depend on any model assumption, and it will become a powerful tool for classification and evolutionary analysis.
This study quantitatively validates the principle that the biological properties associated with a given genotype are determined by the distribution of amino acids. In order to visualize this central law of molecular biology, each protein was represented by a point in 250-dimensional space based on its amino acid distribution. Proteins from the same family are found to cluster together, leading to the principle that the convex hull surrounding protein points from the same family do not intersect with the convex hulls of other protein families. This principle was verified computationally for all available and reliable protein kinases and human proteins. In addition, we generated 2,328,761 figures to show that the convex hulls of different families were disjoint from each other. The classification performs well with high and robust accuracy (95.75% and 97.5%) together with reasonable phylogenetic trees validate our methods further.
Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum).
Rui DongTsinghua UniversityHui ZhengThe University of Illinois at ChicagoKun TianTsinghua UniversityShek-Chung YauThe Hong Kong University of Science and TechnologyWeiguang MaoTsinghua UniversityWenping YuNankai UniversityChangchuan YinThe University of Illinois at ChicagoChenglong YuSouth Australian Health and Medical Research InstituteRong Lucy HeChicago State UniversityJie YangThe University of Illinois at ChicagoStephen S.-T YauTsinghua University
Data Analysis, Bio-Statistics, Bio-Mathematicsmathscidoc:1903.42004
We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.
Yongkun LiDepartment of Mathematical Sciences, Tsinghua UniversityLily HeDepartment of Mathematical Sciences, Tsinghua UniversityRong Lucy HeDepartment of Biological Sciences, Chicago State UniversityStephen S.-T. Yau(CorrespondingDepartment of Mathematical Sciences, Tsinghua University
Data Analysis, Bio-Statistics, Bio-Mathematicsmathscidoc:1903.42003
Zika virus (ZIKV) is a mosquito-borne flavivirus. It was first isolated from Uganda in 1947 and has become an
emergent event since 2007. However, because of the inconsistency of alignment methods, the evolution of
ZIKV remains poorly understood. In this study, we first use the complete protein and an alignment-free method
to build a phylogenetic tree of 87 Zika strains in which Asian, East African, and West African lineages are
characterized. We also use the NS5 protein to construct the genetic relationship among 44 Zika strains. For the
first time, these strains are divided into two clades: African 1 and African 2. This result suggests that ZIKV
originates from Africa, then spread to Asia, Pacific islands, and throughout the Americas. We also perform the
phylogeny analysis for 53 viruses in genus Flavivirus to which ZIKV belongs using complete proteins. Our
conclusion is consistent with the classification by the hosts and transmission vectors.