Prochlorococcus marinus, one of the most abundant marine cyanobacteria in the global ocean, is classified into low-light (LL) and high-light (HL) adapted ecotypes. These two adapted ecotypes differ in their ecophysiological characteristics, especially whether adapted for growth at high-light or low-light intensities. However, some evolutionary relationships of Prochlorococcus phylogeny remain to be resolved, such as whether the strains SS120 and MIT9211 form a monophyletic group. We use the Natural Vector (NV) method to represent the sequence in order to identify the phylogeny of the Prochlorococcus. The natural vector method is alignment free without any model assumptions. This study added the covariances of amino acids in protein sequence to the natural vector method. Based on these new natural vectors, we can compute the Hausdorff distance between the two clades which represents the dissimilarity. This method enables us to systematically analyze both the dataset of ribosomal proteomes and the dataset of 16s-23s rRNA sequences in order to reconstruct the phylogeny of Prochlorococcus. Furthermore, we apply classification to inspect the relationship of SS120 and MIT9211. From the reconstructed phylogenetic trees and classification results, we may conclude that the SS120 does not cluster with MIT9211. This study demonstrates a new method for performing phylogenetic analysis. The results confirm that these two strains do not form a monophyletic clade in the phylogeny of Prochlorococcus.

Structures and functions of proteins play various essential roles in biological processes. The functions of newly discovered proteins can be predicted by comparing their structures with that of known functional proteins. Many approaches have been proposed for measuring the protein structure similarity, such as the template-modeling (TM)-score method, GRaphlet (GR)-Align method as well as the commonly used root-mean-square deviation (RMSD) measures. However, the alignment comparisons between the similarity of protein structure cost much time on large dataset, and the accuracy still have room to improve. In this study, we introduce a new three-dimensional (3D) Yau–Hausdorff distance between any two 3D objects. The (3D) Yau–Hausdorff distance can be used in particular to measure the similarity/dissimilarity of two proteins of any size and does not need aligning and super- imposing two structures. We apply structural similarity to study function similarity and perform phylogenetic analysis on several datasets. The results show that (3D) Yau–Hausdorff distance could serve as a more precise and effective method to discover biological relationships between proteins than other methods on structure comparison.

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).