Comparison Of DNA Sequences Research Articles

Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant.

In solid organ transplantation, donor-derived immune cells are assumed to decline with time after surgery. Whether donor leukocytes persist within kidney transplants or play any role in rejection is unknown, however, in part because of limited techniques for distinguishing recipient from donor cells. Whole-exome sequencing of donor and recipient DNA and single-cell RNA sequencing (scRNA-seq) of five human kidney transplant biopsy cores distinguished immune cell contributions from both participants. DNA-sequence comparisons used single nucleotide variants (SNVs) identified in the exome sequences across all samples. Analysis of expressed SNVs in the scRNA-seq data set distinguished recipient versus donor origin for all 81,139 cells examined. The leukocyte donor/recipient ratio varied with rejection status for macrophages and with time post-transplant for lymphocytes. Recipient macrophages displayed inflammatory activation whereas donor macrophages demonstrated antigen presentation and complement signaling. Recipient-origin T cells expressed cytotoxic and proinflammatory genes consistent with an effector cell phenotype, whereas donor-origin T cells appeared quiescent, expressing oxidative phosphorylation genes. Finally, both donor and recipient T cell clones within the rejecting kidney suggested lymphoid aggregation. The results indicate that donor-origin macrophages and T cells have distinct transcriptional profiles compared with their recipient counterparts, and that donor macrophages can persist for years post-transplantation. Analysis of single nucleotide variants and their expression in single cells provides a powerful novel approach to accurately define leukocyte chimerism in a complex organ such as a transplanted kidney, coupled with the ability to examine transcriptional profiles at single-cell resolution.

Characterization and pathogenicity of fungal trunk pathogens associated with declining of neem (Azadirachta indica A. Juss) trees in Iran

Neem (Azadirachta indica A. Juss.) tree is an important and valuable forestry species and is also ideal for reforesting programs in some countries. Several field surveys were conducted on neem trees in different landscapes in Bandar Abbas (Hormozgan province, southern coast of Iran) to determine fungal species associated with trunk diseases. Wood samples were collected from branches of trees planted in boulevards, public parks, local streets, sidewalks and roadsides with yellowing, defoliation, dieback, canker, gummosis and internal wood discoloration. Fungal isolations were made from discolored wood tissues on potato-dextrose agar supplemented with 0.5 g/L of streptomycin sulphate. Fungal isolates obtained from neem trees, were identified based on morphological characteristics and DNA sequence comparisons. Curvularia hawaiiensis, Neoscytalidium hyalinum, Lasiodiplodia theobromae, Paecilomyces formosus, Paecilomyces dactylethromorphus, Phaeoacremonium venezuelense, P. angustius, P. minimum, P. rubrigenum, P. parasiticum and Pleurostoma richardsiae were the main fungal species recovered from neem trees showing disease symptoms. Pathogenicity of selected species was verified by inoculation of shoots of neem trees under controlled conditions. Neoscytalidium hyalinum was the most aggressive species based on the length of vascular necrosis in the wood. All fungal species, with exception of L. theobromae, are reported here for the first time on neem trees.

No difference in the proteome of racially and geometrically classified scalp hair sample from a South African cohort: Preliminary findings

Differences in the physiological proteome of men of different racial origin is poorly researched, albeit hair is mostly composed of keratins and keratin-associated proteins. Hence, we have carried out label-free, shotgun proteomics analysis on hair samples collected from black African, Caucasian, Asian, and Mixed-Ancestry donors within a heterogeneous population of the Western Cape of South Africa. Further, the same hair was also classified using geometrical measurements. Using both qualitative and quantitative proteomics bioinformatics pipelines, we identified over 450 protein groups (FDR = 0.01). Identified protein classes included keratins, keratin-associated proteins, histone proteins and desmosomes, inter alia. No protein by quantitative proteomic analyses significantly differentiated racial or geometric groups in our cohort. Functional pathway analysis of top-ranking proteins showed enrichment for skin, epidermal and tissue development, as well as intermediate-filament organization. Racial classification is a social construct, and attributing differences in a biologic endpoint to it is both imprecise and valueless in the era of precision medicine. Nonetheless, clarity on the physiological hair proteome could serve as a foundation for using hair proteomics for disease biomarker and targeted therapy identification for precision medicine. For the first time, we established the physiological hair proteome of individuals in a culturally diverse cohort from Africa. SignificanceFor the first time we have been able to characterize the physiological human hair proteome in a culturally diverse South African cohort. We have also identified that proteomics differences were not observed in individual hair samples using our quantitative proteomics bioinformatics pipeline. This outcome supports a widely known notion that DNA sequence comparison often shows that people on each continent are not more genetically similar to one another than to people who come from other continents and that there is more genetic variation in Africa. Hence, adaptive traits such as hair and skin phenotype are not scientifically valid distinctions. Racial classification is believed to be a social construct, and attributing differences in a biologic endpoint to it is both imprecise and valueless in the era of precision medicine. Our preliminary finding would serve as a much-needed foundation for establishing a well-annotated, customized hair proteomics repository for Africans.

Preliminarly Survey Results and Phylogenetic Analysis for Tomato Yellow Leaf Curl Virus and Potato Leaf Roll Virus on Tomato Grown in Adana

Surveys were conducted at tomato production sites in Adana province in 2019. 53 tomato plants have been collected showing the virus symptom due to determining its prevalence. The collected samples were tested for 13 different viral agents harmful to tomatoes using ELISA and RT-PCR methods. 24.52% TYLCV and 9.43% PLRV were detected from the tested samples. When DNA sequencing comparisons are made from RT-PCR products, 98,74% of PLRV isolates in tomato samples collected from Adana province are homogical similarity with Belgium potato isolate (KX364206.1). Also it clustered at 99.37% similar to same branch with New Zealand (GU002341.1) (BLAST at NCBI).

Phenotypic and genotypic characterization of non-typhoidal Salmonella isolated from a Brazilian pork production chain

Pork products are important sources of foodborne non-typhoidal Salmonella in Brazil where antibiotics are commonly used throughout the pork production process and this has the potential to selectively favor antibiotic-resistant strains. We characterized the genotypic and phenotypic diversity of S. enterica isolates (n = 41) that were isolated in Brazil. Isolates were collected from ten swine farms and one slaughterhouse. Whole-genome sequencing and in silico serotyping demonstrated that the S. enterica serovar Typhimurium was the most common serotype (n = 17), but eight additional servoars were identified. Isolates presented high similarity based on comparison of DNA sequences (minimum of 89.6%), and sequence variation grouped according to serotype. Eight multilocus sequence types were identified with ST19 being most common (n = 21). Several plasmids replicons were detected, with Col (RNAI) the most abundant (n = 30), followed by IncR (n = 22), IncI1 (n = 10) and IncA/C2 (n = 10). Minimum inhibitory concentration assays showed that the principle resistance phenotypes were for streptomycin (90.2%), tetracycline (87.8%), ampicillin (80.5%), chloramphenicol (70.7%) and ciprofloxacin (51.2%). Only two isolates were resistant to third-generation cephalosporins and no isolates were resistant to two tested carbapenems. Twenty-six unique antimicrobial-resistance genes were identified with blaTEM-1A and blaTEM-1B likely responsible for most beta-lactam resistance and floR responsible for most chloramphenicol resistance. Six strains were positive for mcr-1. At the time of collection, the sampled farms were adding ciprofloxacin to feed and this may have contributed to the high prevalence of resistance to this antibiotic. The high number of multidrug resistant Salmonella and the presence of multiple resistant genes and plasmids emphasize the diversity of Salmonella in the studied pork chain, specially from serotype Typhimurium.

Streptococcus bovis Contributes to the Development of Colorectal Cancer via Recruiting CD11b⁺TLR-4⁺ Cells.

BackgroundAn increasing number of studies have demonstrated that Streptococcus bovis and its concomitant inflammatory factors concentrate in the intestine in colorectal cancer (CRC). However, the molecular mechanism of S. bovis on colorectal tumorigenesis remains unclear. This study aimed to explore the role of S. bovis in carcinogenesis and its potential mechanism in CRC of mice orally pretreated with S. bovis.Material/MethodsThe colons of experimental mice were collected and evaluated for the extent of neoplasm. In addition, comparative feces DNA sequencing was adopted to verify the abundance change of S. bovis during the progression of CRC in patients.ResultsThe results of this study found that S. bovis is more likely to be present at higher levels in patients with progressive colorectal carcinoma compared to those adenoma patients and healthy volunteers (P<0.05). Pretreatment with S. bovis aggravated tumor formation in mice, resulting in more substantial and a higher number of tumor nodes (P<0.05). A cytokine expression pattern with increased levels of IL-6, Scyb1, Ptgs2, IL-1β, TNF, and Ccl2 was detected in S. bovis pretreated CRC mice (all P<0.05). Furthermore, S. bovis recruited myeloid cells, especially CD11b+TLR-4+ cells, which could promote pro-tumor immunity in the tumor microenvironment (P<0.05).ConclusionsCollectively, our study indicates that S. bovis may induce a suppressive immunity that is conducive to CRC by recruiting tumor-infiltrating CD11b+TLR-4+ cells. In conclusion, S. bovis contributes to colorectal tumorigenesis via recruiting CD11b+TLR-4+ cells.

Ceratocystis quercicola sp. nov. from Quercus variabilis in Korea

During a survey of putative fungal pathogens infecting oak trees in the Gangwon Province of the Republic of Korea, a fungus resembling a Ceratocystis sp. was repeatedly isolated from natural wounds on Quercus variabilis. Morphological comparisons and DNA sequence comparisons based on partial β-tubulin and TEF-1α gene regions showed that the fungus resided in a distinct lineage. This novel Ceratocystis species is described here as C. quercicola sp. nov. This is the first novel species of Ceratocystis to be reported from Korea. A pathogenicity test showed that it can cause lesions on inoculated trees but that it had a very low level of aggressiveness. The discovery of this fungus suggests that additional taxa residing in Ceratocystis are likely to be discovered in Korea in the future.

Phylogenetic Relationships between Phlebiopsis gigantea and Selected Basidiomycota Species Inferred from Partial DNA Sequence of Elongation Factor 1-Alpha Gene

Phlebiopsis gigantea (Fr.) Jülich has been successfully used as a biological control fungus for Heterobasidion annosum (Fr.) Bref., an important pathogen of pine and spruce trees. The P. gigantea species has been known for many years, but our understanding of the relationship between various isolates of this fungus has been substantially improved through the application of DNA sequence comparisons. In this study, relationships between P. gigantea and selected Basidiomycota species was determined, based on elongation factor 1-alpha (EF1α) partial DNA sequence and in silico data. A total of 12 isolates, representing the most representatives of P. gigantea, with diverse geographic distributions and hosts, were included in this study. Phylogenetic trees generated for sequences obtained in this research, grouped the European taxa of P. gigantea and partial sequence of the genome deposed in NCBI database, in a strongly supported clade, basal to the rest of the strains included in the study. P. gigantea isolates originating from Poland, Finland, Sweden, Great Britain and partial sequence of genome formed a monophyletic group. Within this group, isolates of P. gigantea constituted two subclades, showing their partial difference like the two SNPs (single nucleotide polymorphisms) between one and the rest of isolates. The intron and exon relationships among P. gigantea isolates were moreover resolved. The results obtained using the EF1α region should be useful in the selection of more efficient P. gigantea isolates for limiting forest tree root pathogens.

Pattern and timing of diversification in the African freshwater fish genus Distichodus (Characiformes: Distichodontidae)

BackgroundDistichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution.ResultsAnalyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.ConclusionsWe present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

A comparison of anamorphs of some Pachyphlodes species and the type of Chromelosporium: are they congeneric?

There is a question of whether or not the name Chromelosporium competes with the name Pachyphlodes given that both genera exhibit similar conidiogenesis. We address here the question through a comparative study of their anamorphs. The type specimen of C. ochraceum (generic type of Chromelosporium), has been studied and compared to newly collected specimens of two Pachyphlodes species, P. nemoralis and P. citrina (whose identity was confirmed through comparison of ITS DNA sequences) and an unidentified species from the Pachyphlodes–Plicariella lineage. Comparison of the morphology of the Pachyphlodes–Plicariella lineage anamorphs with Chromelosporium ochraceum reveals discriminating characters that may support a generic distinction.

Abstract PR20: A novel combination immunotherapy with a vaccine targeting tumor neoepitopes that mediates immune cascade in murine tumor models

Abstract Clinical successes utilizing checkpoint inhibitors demonstrate the potential of immune-based therapies for the treatment of cancer. Research suggests that these successes are a result of T cells recognizing nonsynonymous mutations uniquely expressed by a patient’s tumor. The advent of comparative tumor-normal DNA sequencing and tumor RNA sequencing for accurate prediction of presented somatic mutations has made it possible to rapidly identify these neoepitopes, allowing for the development of personalized cancer vaccines. However, such vaccines are often ineffective due to the immunosuppressive nature of the tumor microenvironment, and their clinical efficacies would be improved when used in an orchestrated combination approach with additional immune-oncology agents. In the present study, we investigated the combination of three immune-oncology agents, each targeting a unique mechanism of immune therapy, with a vaccine targeting tumor neoepitopes. We combined a neoepitope vaccine, delivered as a peptide or via a novel E2b-deleted adenovirus vehicle, with N-IL15 (previously called ALT-803), an IL-15 superagonist, to enhance the development of antigen-specific immunity; NHS-IL12, a tumor-targeting IL-12 molecule, to promote the maintenance and expansion of T cells within the tumor microenvironment; and PD-L1 blockade to decrease immune cell exhaustion within the tumor microenvironment. This combination therapy resulted in the regression of established tumors, which associated with the generation of robust immunity against neoepitopes contained in the vaccine. It also showed evidence of inducing a neoepitope cascade by causing development of T-cell responses to neoepitopes expressed by the tumor but not contained within the vaccine. This report is the first demonstration of an E2b-deleted adenovirus neoantigen vaccine generating robust immunity. Together, this study demonstrates the importance of a multifaceted, orchestrated treatment regimen to promote the generation of effective antitumor immunity. This abstract is also being presented as Poster A18. Citation Format: Karin L. Lee, Claudia Palena, John Lee, Kayvan Niazi, Andrew Nguyen, Frank Jones, Shahrooz Rabizadeh, Patrick Soon-Shiong, Jeffrey Schlom, Duane H. Hamilton. A novel combination immunotherapy with a vaccine targeting tumor neoepitopes that mediates immune cascade in murine tumor models [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr PR20.

&lt;p&gt;&lt;strong&gt;&lt;em&gt;Leucaenicola&lt;/em&gt;&lt;/strong&gt;&lt;strong&gt; &lt;em&gt;osmanthi&lt;/em&gt; &lt;em&gt;sp&lt;/em&gt;. &lt;em&gt;nov&lt;/em&gt;. (Bambusicolaceae, Pleosporales), causing leaf spot of &lt;em&gt;Osmanthus fragrans&lt;/em&gt; in Taiwan&lt;/strong&gt;&lt;/p&gt;

Osmanthus fragrans naturally occurs in Taiwan, and is now widely cultivated as an ornamental plant. Signs of leaf spots caused by unknown species has been detected on O. fragrans saplings in Nangang District, Taipei City, Taiwan. This investigation aimed to illustrate the fungal species by engaging morphological features, pathogenicity tests, and DNA sequence comparisons for the ITS, LSU, SSU, rpb2 and tef1 gene sequences. A new species is proposed and identified here as Leucaenicola osmanthi. Leucaenicola osmanthi can be differentiated from the phylogenetically close taxa, L. aseptata and L. phraeana, by much larger conidiomata, conidiogenous cells and conidia. Moreover, this is the first report of a species belonging to Leucaenicola on Osmanthus fragrans in Taiwan.

Correction to: Isolation, Characterization, and Expression Profiling of Nucleoside Diphosphate Kinase Gene from Tall Fescue (Festuca arundinacea Schreb.) (FaNDPK) under Salt Stress

Fifty tall fescue (Festuca arundinacea Schreb.) half-sib families were screened under salinity stress during germination stage, and five tolerant and five sensitive half-sib families were selected. After studying morphological and biochemical characteristics of 10 selected families, the most salt-tolerant family was used for gene expression analysis. Real-time PCR analysis showed that the NDPK expression in plants treated by 200-mM sodium chloride has increased 36.782-fold greater than that in the control ones. The full length of encoding region of NDPK in tall fescue was obtained using the rapid amplification of cDNA ends technique. The homology comparison of DNA sequences, deduced amino acid sequences, and protein sequences were carried out using CLASTALW program in NCBI. The fragment composed of 822 nucleotides (gene’s ORF was 508 nucleotides), and corresponding protein consist 168 amino acids with a predicted molecular mass of 19.4 kD. Blast search for isolated fragment showed that our sequenced fragment is highly similar to UMP/CMP kinase of Oryza sativa japonica (95%). In Blastp, the amino acid sequence of isolated fragment was similar to UMP/CMP kinase of Sorghum bicolor (95%). The results of study confirm that the NDPK is related to UMP/CMP kinase.

Two novel Rickettsia species of soft ticks in North Africa: ‘Candidatus Rickettsia africaseptentrionalis’ and ‘Candidatus Rickettsia mauretanica’

Rickettsia are obligate intracellular bacteria often reported from hard ticks but more rarely from soft ticks. In this study, we detected in Northern Africa two putatively novel Rickettsia species in soft tick species of the Ornithodoros erraticus complex: Ornithodoros occidentalis from Morocco, Ornithodoros erraticus from Algeria and Ornithodoros normandi from Tunisia. We characterized these two novel Rickettsia species on the basis of comparative DNA sequence analyses and phylogenetics of four genes (gltA, 16S rRNA, coxA and ompB). These Rickettsia, provisionally named ‘Candidatus Rickettsia africaseptentrionalis’ and ‘Candidatus Rickettsia mauretanica’, differed in nucleotide sequence from those of other Rickettsia species by 0.38–21.43 % depending on the gene examined. Phylogenetics further showed that the two novel Rickettsia species are closely related to each other and represent sister taxa to R. hoogstraalii, R. felis and R. asembonensis within the transitional Rickettsia group. While Ornithodoros host species of ‘Candidatus Rickettsia africaseptentrionalis’ and ‘Candidatus Rickettsia mauretanica’ are among the most common soft ticks to bite humans, their pathogenicity remains to be investigated.

CARDUUS CINEREUS (ASTERACEAE) – NEW TO NORTH AMERICA

Carduus cinereus M.Bieb. populations have been discovered in the Hells Canyon Wilderness of northeastern Oregon and western Idaho. These plants were initially identified as C. pycnocephalus L. They are distinguished from that species by loosely clustered, usually pedunculate, heads and by scarious-margined phyllaries. These plants are genetically distant from other North American Carduus species (<94% similarity) based on DNA sequence comparisons of the internal transcribed spacers between the 18S and 26S nuclear rDNA regions. Carduus cinereus is new to North America. A revised key to the species of Carduus in North America is presented.

Cryphonectriaceae on Myrtales in China: phylogeny, host range, and pathogenicity.

Plantation-grown Eucalyptus (Myrtaceae) and other trees residing in the Myrtales have been widely planted in southern China. These fungal pathogens include species of Cryphonectriaceae that are well-known to cause stem and branch canker disease on Myrtales trees. During recent disease surveys in southern China, sporocarps with typical characteristics of Cryphonectriaceae were observed on the surfaces of cankers on the stems and branches of Myrtales trees. In this study, a total of 164 Cryphonectriaceae isolates were identified based on comparisons of DNA sequences of the partial conserved nuclear large subunit (LSU) ribosomal DNA, internal transcribed spacer (ITS) regions including the 5.8S gene of the ribosomal DNA operon, two regions of the β-tubulin (tub2/tub1) gene, and the translation elongation factor 1-alpha (tef1) gene region, as well as their morphological characteristics. The results showed that eight species reside in four genera of Cryphonectriaceae occurring on the genera Eucalyptus, Melastoma (Melastomataceae), Psidium (Myrtaceae), Syzygium (Myrtaceae), and Terminalia (Combretaceae) in Myrtales. These fungal species include Chrysoporthe deuterocubensis, Celoporthe syzygii, Cel. eucalypti, Cel. guangdongensis, Cel. cerciana, a new genus and two new species, as well as one new species of Aurifilum. These new taxa are hereby described as Parvosmorbus gen. nov., Par. eucalypti sp. nov., Par. guangdongensis sp. nov., and Aurifilum terminali sp. nov. Pathogenicity tests showed that the eight species of Cryphonectriaceae are pathogenic to two Eucalyptus hybrid seedlings, Melastoma sanguineum branches, and Psidium guajava and Syzygium jambos seedlings. The overall data showed that Chr. deuterocubensis is the most aggressive, followed by Par. eucalypti. Significant differences in tolerance were observed between the two tested Eucalyptus hybrid genotypes, suggesting that disease-tolerant genotypes can be selected for disease management in the Eucalyptus industry.

Modified k-string in composition vector method for DNA sequence comparison based on maximum entropy principle

The Composition Vector method is a type of alignment-free methods for sequence comparison. The proposed method is based on modified k-string method, which uses the ratio of frequencies of all possible sub-words of length k in a DNA sequence to compare two sequences. We have proposed a scheme based on modified formulas for sequence comparison considering principle of maximum entropy. There exist several formulas for the purpose however the one maximizing the entropy was selected for the study. It leads to a unified approach for sequence comparison. The obtained results have been analyzed and compared with existing composition vector and K-string methods by drawing phylogenetic trees. The results show that the proposed scheme performs better in comparison to existing methods.

Spiophanes adriaticus, a new species from the Mediterranean Sea

AbstractMorphological and genetic investigations have led to the identification of Spiophanes adriaticus sp. nov. (Polychaeta: Spionidae) from the North Adriatic Sea (Central Mediterranean). A total of 81 specimens were recorded along the sublittoral zone between 8 and 27.5 m of depth. This species differs from other congeners by having: two pairs of black eyes, a cirriform occipital antenna, dorsal ciliated organs as thin bands usually extending to chaetigers 11–12, dorsal ciliated crests from chaetiger 14–17, undulate glandular opening on chaetigers 5–7, unhooded hooks from the 15th chaetiger and Y shaped tubes. A detailed description and illustrations are provided for the new species. Through DNA barcoding results and comparison of DNA sequences of the new species with those of other congeners available in the GenBank database, the validity of the new finding was confirmed. Spiophanes adriaticus sp. nov. represents the eighth species of Spiophanes recorded for the Mediterranean Sea. A key for the identification of Mediterranean Spiophanes species is also provided.

MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis.

Machine Learning with Digital Signal Processing and Graphical User Interface (MLDSP-GUI) is an open-source, alignment-free, ultrafast, computationally lightweight, and standalone software tool with an interactive GUI for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others. MLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/. Supplementary data are available at Bioinformatics online.

Genome sequence comparison under a new form of tri-nucleotide representation based on bio-chemical properties of nucleotides

Genetic sequence analysis, classification of genome sequence and evolutionary relationship between species using their biological sequences, are the emerging research domain in Bioinformatics. Several methods have already been applied to DNA sequence comparison under tri-nucleotide representation. In this paper, a new form of tri-nucleotide representation is proposed for sequence comparison. The comparison does not depend on the alignment of the sequences. In this representation, the bio-chemical properties of the nucleotides are considered. The novelty of this method is that the sequences of unequal lengths are represented by vectors of the same length and each of the tri-nucleotide formed out of the given sequence has its unique representation. To validate the proposed method, it is verified on several data sets related to mammalians, viruses and bacteria. The results of this method are further compared with those obtained by methods such as probabilistic method, natural vector method, Fourier power spectrum method, multiple encoding vector method, and feature frequency profiles method. Moreover, this method produces accurate phylogeny in all the cases. It is also proved that the time complexity of the present method is less.