Graphical representation methods: How well do they discriminate between homologous gene sequences?

Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes.

A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines.

The growing incidences of new viral diseases and increasingly frequent viral epidemics have strained therapeutic and preventive measures; the high mutability of viral genes puts additional strains on developmental efforts. Given the high cost and time requirements for new drugs development, vaccines remain as a viable alternative, but there too traditional techniques of live-attenuated or inactivated vaccines have the danger of allergenic reactions and others. Peptide vaccines have, over the last several years, begun to be looked on as more appropriate alternatives, which are economically affordable, require less time for development and hold the promise of multi-valent dosages. The developments in bioinformatics, proteomics, immunogenomics, structural biology and other sciences have spurred the growth of vaccinomics where computer assisted approaches serve to identify suitable peptide targets for eventual development of vaccines. In this mini-review we give a brief overview of some of the recent trends in computer assisted vaccine development with emphasis on the primary selection procedures of probable peptide candidates for vaccine development.

Descriptors of 2D-dynamic graphs as a classification tool of DNA sequences.

A new tool of the classification of DNA sequences is introduced. The method is based on 2D-dynamic graphs and their descriptors. Using the descriptors created by centers of masses, moments of inertia, angles between the x axis and the principal axis of inertia of the 2D-dynamic graphs one can obtain classification diagrams in which similar sequences are clustered in separated areas.

Mapping Biomolecular Sequences: Graphical Representations - Their Origins, Applications and Future Prospects.

The exponential growth in the depositories of biological sequence data has generated an urgent need to store, retrieve and analyse the data efficiently and effectively for which the standard practice of using alignment procedures are not adequate due to high demand on computing resources and time. Graphical representation of sequences has become one of the most popular alignment-free strategies to analyse the biological sequences where each basic unit of the sequences - the bases adenine, cytosine, guanine and thymine for DNA/RNA, and the 20 amino acids for proteins - are plotted on a multi-dimensional grid. The resulting curve in 2D and 3D space and the implied graph in higher dimensions provide a perception of the underlying information of the sequences through visual inspection; numerical analyses, in geometrical or matrix terms, of the plots provide a measure of comparison between sequences and thus enable study of sequence hierarchies. The new approach has also enabled studies of comparisons of DNA sequences over many thousands of bases and provided new insights into the structure of the base compositions of DNA sequences. In this article we review in brief the origins and applications of graphical representations and highlight the future perspectives in this field.

Combatting future variants of SARS-CoV-2 using an in-silico peptide vaccine approach by targeting the spike protein.

The far-reaching effects of the SARS-CoV-2 pandemic have crippled the progress of the world today. With the introduction of newer and newer mutated variants of the virus, it has become necessary to have a vaccine that remains useful against all the mutated strains of SARS-CoV-2. In this regard, peptide vaccines turn out to be a cheap alternative to the traditionally designed vaccines owing to their much quicker and computationally easier, and more robust design procedures. Here, in this article, we hypothesize that there are three possible peptide vaccine regions that can be targeted to prevent the surge of SARS-CoV-2. The candidates that were selected, were surface-exposed and were not sequestered by any neighbouring amino acids. They were also found to be capable of generating both B-cell and T-cell immune responses. Most importantly, none of them contains any spike protein mutation of the currently prevailing variants of SARS-CoV-2. From these findings, we have therefore concluded that these three regions can be used in wet labs for peptide vaccine design against the upcoming strains of SARS-CoV-2.

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2.

The design for vaccines using in silico analysis of genomic data of different viruses has taken many different paths, but lack of any precise computational approach has constrained them to alignment methods and some alignment-free techniques. In this work, a precise computational approach has been established wherein two new mathematical parameters have been suggested to identify the highly conserved and surface-exposed regions which are spread over a large region of the surface protein of the virus so that one can determine possible peptide vaccine candidates from those regions. The first parameter, w, is the sum of the normalized values of the measure of surface accessibility and the normalized measure of conservativeness, and the second parameter is the area of a triangle formed by a mathematical model named 2D Polygon Representation. This method has been, therefore, used to determine possible vaccine targets against SARS-CoV-2 by considering its surface-situated spike glycoprotein. The results of this model have been verified by a parallel analysis using the older approach of manually estimating the graphs describing the variation of conservativeness and surface-exposure across the protein sequence. Furthermore, the working of the method has been tested by applying it to find out peptide vaccine candidates for Zika and Hendra viruses respectively. A satisfactory consistency of the model results with pre-established results for both the test cases shows that this in silico alignment-free analysis proposed by the model is suitable not only to determine vaccine targets against SARS-CoV-2 but also ready to extend against other viruses.

Clustering of Zika Viruses Originating from Different Geographical Regions using Computational Sequence Descriptors.

BACKGROUND: In this report, we consider a data set, which consists of 310 Zika virus genome sequences taken from different continents, Africa, Asia and South America. The sequences, which were compiled from GenBank, were derived from the host cells of different mammalian species (Simiiformes, Aedes opok, Aedes africanus, Aedes luteocephalus, Aedes dalzieli, Aedes aegypti, and Homo sapiens). METHODS: For chemometrical treatment, the sequences have been represented by sequence descriptors derived from their graphs or neighborhood matrices. The set was analyzed with three chemometrical methods: Mahalanobis distances, principal component analysis (PCA) and self organizing maps (SOM). A good separation of samples with respect to the region of origin was observed using these three methods. RESULTS: Study of 310 Zika virus genome sequences from different continents. To characterize and compare Zika virus sequences from around the world using alignment-free sequence comparison and chemometrical methods. CONCLUSION: Mahalanobis distance analysis, self organizing maps, principal components were used to carry out the chemometrical analyses of the Zika sequence data. Genome sequences are clustered with respect to the region of origin (continent, country). Africa samples are well separated from Asian and South American ones.

Identification and computational analysis of mutations in SARS-CoV-2.

SARS-CoV-2 infection has become a worldwide pandemic and is spreading rapidly to people across the globe. To combat the situation, vaccine design is the essential solution. Mutation in the virus genome plays an important role in limiting the working life of a vaccine. In this study, we have identified several mutated clusters in the structural proteins of the virus through our novel 2D Polar plot and qR characterization descriptor. We have also studied several biochemical properties of the proteins to explore the dynamics of evolution of these mutations. This study would be helpful to understand further new mutations in the virus and would facilitate the process of designing a sustainable vaccine against the deadly virus.

Cluster Analysis of Coronavirus Sequences using Computational Sequence Descriptors: With Applications to SARS, MERS and SARS-CoV-2 (CoVID-19).

INTRODUCTION: Coronaviruses comprise a group of enveloped, positive-sense single-stranded RNA viruses that infect humans as well as a wide range of animals. The study was performed on a set of 573 sequences belonging to SARS, MERS and SARS-CoV-2 (CoVID-19) viruses. The sequences were represented with alignment-free sequence descriptors and analyzed with different chemometric methods: Euclidean/Mahalanobis distances, principal component analysis and self-organizing maps (Kohonen networks). We report the cluster structures of the data. The sequences are well-clustered regarding the type of virus; however, some of them show the tendency to belong to more than one virus type. BACKGROUND: This is a study of 573 genome sequences belonging to SARS, MERS and SARS-- CoV-2 (CoVID-19) coronaviruses. OBJECTIVES: The aim was to compare the virus sequences, which originate from different places around the world. METHODS: The study used alignment free sequence descriptors for the representation of sequences and chemometric methods for analyzing clusters. RESULTS: Majority of genome sequences are clustered with respect to the virus type, but some of them are outliers. CONCLUSION: We indicate 71 sequences, which tend to belong to more than one cluster.

Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase.

BACKGROUND: Catalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene. RESULTS: We extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514) and H1N1 swine flu sequences (425) accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM) for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA) that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure. CONCLUSION: The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure.

Computational Methodology for Peptide Vaccine Design for Zika Virus: A Bioinformatics Approach.

With the increasing frequency of viral epidemics, vaccines to augment the human immune response system have been the medium of choice to combat viral infections. The tragic consequences of the Zika virus pandemic in South and Central America a few years ago brought the issues into sharper focus. While traditional vaccine development is time-consuming and expensive, recent advances in information technology, immunoinformatics, genetics, bioinformatics, and related sciences have opened the doors to new paradigms in vaccine design and applications.Peptide vaccines are one group of the new approaches to vaccine formulation. In this chapter, we discuss the various issues involved in the design of peptide vaccines and their advantages and shortcomings, with special reference to the Zika virus for which no drugs or vaccines are as yet available. In the process, we outline our work in this field giving a detailed step-by-step description of the protocol we follow for such vaccine design so that interested researchers can easily follow them and do their own designing. Several flowcharts and figures are included to provide a background of the software to be used and results to be anticipated.

Computational study of dispersion and extent of mutated and duplicated sequences of the H5N1 influenza neuraminidase over the period 1997-2008.

Study of mutational changes in neuraminidase (NA) gene sequences is important to track the effectiveness of the inhibitors to the H5N1 avian flu virus that targets this component of the viral apparatus. Our analysis based on numerical characterization studies of 682 complete neuraminidase gene and protein sequences available in the database, updated to March 2009, and which extends our previous work based on a sample of 173 sequences has revealed several interesting features. We have noticed that identical sequences have appeared over significant distances in space and time, raising the need for a deeper understanding of the longevity of such viral strains in the environment. Structural sections like transmembrane, stalk, body, and C-terminal tail regions have shown independent recombinations between strains from various species including human and avian hosts highlighting influenza's flexibility in host selection and recombination. Our analysis confirmed a biased nature in mutational accumulation in structural segments: a highly conserved 50-base C-terminal tail section identified in our earlier paper seems to accumulate mutational changes at a rate of about a fifth to an eighth of transmembrane and stalk regions, although the length is about half of these. Parallel study of the equivalent section to the C-terminal region in protein sequences reveals only 13 separate varieties, and all the other 669 sequences are duplicates to three of these varieties showing the highly conserved nature of this segment. Our analysis of active site related bases and amino acids showed highly conserved characteristic of those constructs, whereas the rest of the segments demonstrated rather large mutational changes. These kinds of high level of mutation in major part of the H5N1 NA sequences and recombinations within structural segments coupled with strong conservation of a few select segments show that the potential of rapid mutations to more virulent forms of this variety of avian flu continue to remain of concern, especially with the possibility of long duration dormancy of some of these viral strains, whereas islands of highly conserved segments could signify potential regions for inhibitor designs.

Base Distribution in Dengue Nucleotide Sequences Differs Significantly from Other Mosquito-Borne Human-Infecting Flavivirus Members.

INTRODUCTION: Among the mosquito-borne human-infecting flavivirus species that include Zika, West Nile, yellow fever, Japanese encephalitis and Dengue viruses, the Zika virus is found to be closest to Dengue virus, sharing the same clade in the Flavivirus phylogenetic tree. We consider these five flaviviruses and on closer examination in our analyses, the nucleotide sequences of the Dengue viral genes (envelope and NS5) and genomes are seen to be quite widely different from the other four flaviviruses. We consider the extent of this distinction and determine the advantage and/or disadvantage such differences may confer upon the Dengue viral pathogenesis. METHODS: We have primarily used a 2D graphical representation technique to show the differences in base distributions in these five flaviviruses and subsequently, obtained quantitative estimates of the differences. Similarity/dissimilarity between the viruses based on the genes were also determined which showed that the differences with the Dengue genes are more pronounced. RESULTS: We found that the Dengue viruses compared to the other four flaviviruses spread rapidly worldwide and became endemic in various regions with small alterations in sequence composition relative to the host populations as revealed by codon usage biases and phylogenetic examination. CONCLUSION: We conclude that the Dengue genes are indeed more widely separated from the other aforementioned mosquito-borne human-infecting flaviviruses due to excess adenine component, a feature that is sparse in the literature. Such excesses have a bearing on drug and vaccine, especially peptide vaccine, development and should be considered appropriately.

Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus.

Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.

Epidemics and Peptide Vaccine Response: A Brief Review.

We briefly review the situations arising out of epidemics that erupt rather suddenly, threatening life and livelihoods of humans. Ebola, Zika and the Nipah virus outbreaks are recent examples where the viral epidemics have led to considerably high degree of fatalities or debilitating consequences. The problems are accentuated by a lack of drugs or vaccines effective against the new and emergent viruses, and the inordinate amount of temporal and financial resources that are required to combat the novel pathogens. Progress in computational, biological and informational sciences have made it possible to consider design of synthetic vaccines that can be rapidly developed and deployed to help stem the damages. In this review, we consider the pros and cons of this new paradigm and suggest a new system where the manufacturing process can be decentralized to provide more targeted vaccines to meet the urgent needs of protection in case of a rampaging epidemic.

A Bioinformatics approach to designing a Zika virus vaccine.

The Zika virus infections have reached epidemic proportions in the Latin American countries causing severe birth defects and neurological disorders. While several organizations have begun research into design of prophylactic vaccines and therapeutic drugs, computer assisted methods with adequate data resources can be expected to assist in these measures to reduce lead times through bioinformatics approaches. Using 60 sequences of the Zika virus envelope protein available in the GenBank database, our analysis with numerical characterization techniques and several web based bioinformatics servers identified four peptide stretches on the Zika virus envelope protein that are well conserved and surface exposed and are predicted to have reasonable epitope binding efficiency. These peptides can be expected to form the basis for a nascent peptide vaccine which, enhanced by incorporation of suitable adjuvants, can elicit immune response against the Zika virus infections.

Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges.

BACKGROUND: The influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during replication when, if two viral strains infect a cell, a part of a gene from the second viral strain can be copied into the growing progeny of a gene of the first viral strain as replacement leading to a new variety of the virus. This template switching between the same genes of the two strains is known as homologous recombination. While genetic drift and shift are well-understood, the presence or absence of intra-segment homologous recombination in influenza genomes is controversial. CONTEXT AND PURPOSE OF STUDY: We are interested to study the possibility of subunit-wise homologous recombination. The idea is that where well-defined subunits are separated by consensus sequences, it might be possible for template switching to take place at such junctions. The influenza hemagglutinin gene has basically two subunits, HA1 and HA2, with HA1 being mostly surface exposed and containing the active site for binding to cells, while HA2 secures the hemagglutinin to the viral coat. We undertook a thorough search of the major human infecting influenza hemagglutinin gene sequences, viz., the H1N1, H5N1, H3N2 and H7N9 subtypes, over the period 2010-2014 in Asia to determine if certain sequences could be identified that had HA1 from a previous strain and HA2 from another. RESULTS: Our search yielded several instances where sequence identities between segments of various strains could be interpreted as indicating possibilities of segment exchange. In some cases, on closer examination they turn out to differ by a few mutations in each segment, due perhaps to the short time span of our database. CONCLUSIONS AND POTENTIAL IMPLICATIONS: The study reported here, and in combination with our earlier observations on the neuraminidase, shows that subunit-wise recombination-like events in the influenza genes may be occurring more often than have been accounted for and merits further detailed studies.

Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus.

Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities. Using the L1 capsid protein sequences, we identified several peptides for potential vaccine design for HPV 16, 18, 33, 35, 45, and 11 types. Although there are concerns about the epitope-binding affinities for the peptides identified in this process, the technique indicates possibilities of multivalent, adjuvanted, peptide vaccines against a wider range of HPV types, and tailor-made different combinations of the peptides to address frequency variations of types over different population groups as required for prophylaxis and at lower cost than are in use at the present time.

Characterizing the Zika Virus Genome - A Bioinformatics Study.

BACKGROUND: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date. OBJECTIVE: To carry out a bioinformatics study of the available Zika virus genomic sequences to characterize the virus. METHOD: 2D graphical representation method is used for visual rendering and compute sequence parameters and descriptors of the African and Asian-American groups of the Zika viruses to characterize the sequences. We also used MEGA5.2 and other software to compute various biological properties of interest like phylogenetic relationships, transition-transversion ratios, amino acid usage, codon usage bias and hydropathy index of the Zika genomes and virions. RESULTS: The phylogenetic relationships show that the African and Asian-American Zika virus genomes are grouped in two clades. The 2D plots of typical genomes of these types also show dramatic differences indicating that the gene sequences at the 5'-end coding regions for the structural proteins are rather strongly conserved. Among other characteristics, the transition/transversion ratio matrices for the sequences in each of the two clades show that analogous to the dengue virus, the transition rates are about 10 to 15 times the transversion rates. CONCLUSION: These findings are important for computer-assisted approaches towards surveillance of emerging Zika virus strains as well as in the design of drugs and vaccines to combat the growth and spread of the Zika virus.