K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.

Abstract:

:In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis.

journal_name

Genes (Basel)

journal_title

Genes

authors

Sievers A,Bosiek K,Bisch M,Dreessen C,Riedel J,Froß P,Hausmann M,Hildenbrand G

doi

10.3390/genes8040122

subject

Has Abstract

pub_date

2017-04-19 00:00:00

issue

4

issn

2073-4425

pii

genes8040122

journal_volume

8

pub_type

杂志文章

相关文献

Genes文献大全
  • NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files.

    abstract::High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems. Unfortunately, however, new data generation tends to significantly outpace data re-utilization, and most high throughput datasets are only rarely used in subsequent studies or to generate n...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10060423

    authors: Halajyan A,Weingart N,Yeahia M,Loza-Coll M

    更新日期:2019-06-01 00:00:00

  • Constructing the Microbial Association Network from Large-Scale Time Series Data Using Granger Causality.

    abstract::The increasing availability of large-scale time series data allows the inference of microbial community dynamics by association network analysis. However, correlation-based association network analyses are noninformative of causal, mediating and time-dependent relationships between microbial community functional facto...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10030216

    authors: Ai D,Li X,Liu G,Liang X,Xia LC

    更新日期:2019-03-14 00:00:00

  • TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes.

    abstract::Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85-90% reactivate telomerase, while 10-15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between b...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11070834

    authors: Armendáriz-Castillo I,López-Cortés A,García-Cárdenas J,Guevara-Ramírez P,Leone PE,Pérez-Villa A,Yumiceba V,Zambrano AK,Guerrero S,Paz-Y-Miño C

    更新日期:2020-07-21 00:00:00

  • DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation.

    abstract::DNA methyltransferases (DNMTs) play an essential role in DNA methylation and transcriptional regulation in the genome. DNMTs, along with other poorly studied elements, modulate the dynamic DNA methylation patterns of embryonic and adult cells. We summarize the current knowledge on the molecular mechanism of DNMTs' fun...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes11111336

    authors: Loaeza-Loaeza J,Beltran AS,Hernández-Sotelo D

    更新日期:2020-11-12 00:00:00

  • Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System.

    abstract::The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successf...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11060708

    authors: Palencia-Madrid L,Xavier C,de la Puente M,Hohoff C,Phillips C,Kayser M,Parson W

    更新日期:2020-06-26 00:00:00

  • DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age.

    abstract::We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from con...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8060152

    authors: Kozlenkov A,Jaffe AE,Timashpolsky A,Apontes P,Rudchenko S,Barbu M,Byne W,Hurd YL,Horvath S,Dracheva S

    更新日期:2017-05-30 00:00:00

  • Canine Melanomas as Models for Human Melanomas: Clinical, Histological, and Genetic Comparison.

    abstract::Despite recent genetic advances and numerous ongoing therapeutic trials, malignant melanoma remains fatal, and prognostic factors as well as more efficient treatments are needed. The development of such research strongly depends on the availability of appropriate models recapitulating all the features of human melanom...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes10070501

    authors: Prouteau A,André C

    更新日期:2019-06-30 00:00:00

  • A Comparative Analysis of CD32A and CD16A Polymorphisms in Relation to Autoimmune Responses in Pemphigus Diseases and Subepithelial Autoimmune Blistering Disorders.

    abstract::Autoimmune blistering dermatoses (ABDs) are characterized by autoantibodies to keratinocyte surface antigens and molecules within the dermal-epidermal junction causing disruption of skin integrity. The affinity of Fc receptors (FcRs) causing an autoimmune response in ABDs may vary based on single-nucleotide polymorphi...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11040371

    authors: Gornowicz-Porowska J,Kowalczyk MJ,Seraszek-Jaros A,Bowszyc-Dmochowska M,Kaczmarek E,Żaba R,Dmochowski M

    更新日期:2020-03-30 00:00:00

  • Molecular Strategies for RPGR Gene Therapy.

    abstract::Mutations affecting the Retinitis Pigmentosa GTPase Regulator (RPGR) gene are the commonest cause of X-linked and recessive retinitis pigmentosa (RP), accounting for 10%-20% of all cases of RP. The phenotype is one of the most severe amongst all causes of RP, characteristic for its early onset and rapid progression to...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes10090674

    authors: Cehajic Kapetanovic J,McClements ME,Martinez-Fernandez de la Camara C,MacLaren RE

    更新日期:2019-09-04 00:00:00

  • The Epigenetics Dilemma.

    abstract::This special issue of Genes demonstrates clearly that research in epigenetics has proceeded at a very rapid pace in the last decade. [...]. ...

    journal_title:Genes

    pub_type: 社论

    doi:10.3390/genes11010023

    authors: Grunau C,Le Luyer J,Laporte M,Joly D

    更新日期:2019-12-23 00:00:00

  • Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler.

    abstract::There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to pe...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11060664

    authors: Wee SK,Sivalingam SP,Yap EPH

    更新日期:2020-06-18 00:00:00

  • The Tyrosyl-DNA Phosphodiesterase 1β (Tdp1β) Gene Discloses an Early Response to Abiotic Stresses.

    abstract::Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is involved in DNA repair pathways as it mends the topoisomerase I-DNA covalent complexes. In plants, a small Tdp1 gene family, composed by Tdp1α and Tdp1β genes, was identified, but the roles of these genes in abiotic stress responses are not fully understood. To investigate the...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8110305

    authors: Sabatini ME,Pagano A,Araùjo S,Balestrazzi A,Macovei A

    更新日期:2017-11-03 00:00:00

  • Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians.

    abstract::In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes10090646

    authors: Wollenberg Valero KC,Marshall JC,Bastiaans E,Caccone A,Camargo A,Morando M,Niemiller ML,Pabijan M,Russello MA,Sinervo B,Werneck FP,Sites JW,Jr.,Wiens JJ,Steinfartz S

    更新日期:2019-08-26 00:00:00

  • mRNA Expression and DNA Methylation Analysis of Serotonin Receptor 2A (HTR2A) in the Human Schizophrenic Brain.

    abstract::Serotonin receptor 2A (HTR2A) is an important signalling factor implicated in cognitive functions and known to be associated with schizophrenia. The biological significance of HTR2A in schizophrenia remains unclear as molecular analyses including genetic association, mRNA expression and methylation studies have report...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8010014

    authors: Cheah SY,Lawford BR,Young RM,Morris CP,Voisey J

    更新日期:2017-01-04 00:00:00

  • Investigation of Precise Molecular Mechanistic Action of Tobacco-Associated Carcinogen `NNK´ Induced Carcinogenesis: A System Biology Approach.

    abstract::Cancer is the second deadliest disease listed by the WHO. One of the major causes of cancer disease is tobacco and consumption possibly due to its main component, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). A plethora of studies have been conducted in the past aiming to decipher the association of NNK with o...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10080564

    authors: Anukriti.,Dhasmana A,Uniyal S,Somvanshi P,Bhardwaj U,Gupta M,Haque S,Lohani M,Kumar D,Ruokolainen J,Kesari KK

    更新日期:2019-07-26 00:00:00

  • Novel Mutations in CLPP, LARS2, CDH23, and COL4A5 Identified in Familial Cases of Prelingual Hearing Loss.

    abstract::We report the underlying genetic causes of prelingual hearing loss (HL) segregating in eight large consanguineous families, ascertained from the Punjab province of Pakistan. Exome sequencing followed by segregation analysis revealed seven potentially pathogenic variants, including four novel alleles c.257G>A, c.6083A>...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11090978

    authors: Zafar S,Shahzad M,Ishaq R,Yousaf A,Shaikh RS,Akram J,Ahmed ZM,Riazuddin S

    更新日期:2020-08-22 00:00:00

  • Transmission and Drive Involving Parasitic B Chromosomes.

    abstract::B chromosomes (Bs) are enigmatic additional elements in the genomes of thousands of species of plants, animals, and fungi. How do these non-essential, harmful, and parasitic chromosomes maintain their presence in their hosts, making demands on all the essential functions of their host genomes? The answer seems to be t...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes9080388

    authors: Jones RN

    更新日期:2018-07-31 00:00:00

  • Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Chinese Perch, Siniperca chuatsi.

    abstract::Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Ch...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10020178

    authors: Lv LY,Liang XF,He S

    更新日期:2019-02-25 00:00:00

  • The role of bromodomain proteins in regulating gene expression.

    abstract::Histone modifications are important in regulating gene expression in eukaryotes. Of the numerous histone modifications which have been identified, acetylation is one of the best characterised and is generally associated with active genes. Histone acetylation can directly affect chromatin structure by neutralising char...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes3020320

    authors: Josling GA,Selvarajah SA,Petter M,Duffy MF

    更新日期:2012-05-29 00:00:00

  • Environmental Change-Dependent Inherited Epigenetic Response.

    abstract::Epigenetic modifications are a mechanism conveying environmental information to subsequent generations via parental germ lines. Research on epigenetic responses to environmental changes in wild mammals has been widely neglected, as well as studies that compare responses to changes in different environmental factors. H...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10010004

    authors: Weyrich A,Lenz D,Fickel J

    更新日期:2018-12-21 00:00:00

  • A Bi-Exponential Repair Algorithm for Radiation-Induced Double-Strand Breaks: Application to Simulation of Chromosome Aberrations.

    abstract:BACKGROUND:Radiation induces DNA double-strand breaks (DSBs), and chromosome aberrations (CA) form during the DSBs repair process. Several methods have been used to model the repair kinetics of DSBs including the bi-exponential model, i.e., N(t) = N1exp(-t/τ1) + N2exp(-t/τ2), where N(t) is the number of breaks at time ...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10110936

    authors: Plante I,Slaba T,Shavers Z,Hada M

    更新日期:2019-11-16 00:00:00

  • An Introduction to Systems Analytics and Integration of Big Omics Data.

    abstract::A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]. ...

    journal_title:Genes

    pub_type: 社论

    doi:10.3390/genes11030245

    authors: Hardiman G

    更新日期:2020-02-26 00:00:00

  • Hyperphagia and Obesity in Prader⁻Willi Syndrome: PCSK1 Deficiency and Beyond?

    abstract::Prader⁻Willi syndrome (PWS) is a complex genetic disorder that, besides cognitive impairments, is characterized by hyperphagia, obesity, hypogonadism, and growth impairment. Proprotein convertase subtilisin/kexin type 1 (PCSK1) deficiency, a rare recessive congenital disorder, partially overlaps phenotypically with PW...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes9060288

    authors: Ramos-Molina B,Molina-Vega M,Fernández-García JC,Creemers JW

    更新日期:2018-06-07 00:00:00

  • Development of Molecular Marker Linked with Bacterial Fruit Blotch Resistance in Melon (Cucumis melo L.).

    abstract::Bacterial fruit blotch (BFB) causes losses in melon marketable yield. However, until now, there has been no information about the genetic loci responsible for resistance to the disease or their pattern of inheritance. We determined the inheritance pattern of BFB resistance from a segregating population of 491 F2 indiv...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11020220

    authors: Islam MR,Hossain MR,Jesse DMI,Jung HJ,Kim HT,Park JI,Nou IS

    更新日期:2020-02-19 00:00:00

  • Genetic Association between Amyotrophic Lateral Sclerosis and Cancer.

    abstract::Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. An ALS drug, Riluzole, has been shown to induce two different anticancer effects on hepatocellular carcinoma (HCC). In light of this finding, we explore the relationship between ALS and cancer, especially for HCC, from the molecular biological v...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8100243

    authors: Taguchi YH,Wang H

    更新日期:2017-09-27 00:00:00

  • Selection of Suitable Reference Genes for RT-qPCR Gene Expression Analysis in Siberian Wild Rye (Elymus sibiricus) under Different Experimental Conditions.

    abstract::Elymus sibiricus, which is a perennial and self-pollinated grass, is the typical species of the genus Elymus, which plays an important role in forage production and ecological restoration. No reports have, so far, systematically described the selection of optimal reference genes for reverse transcriptase quantitative ...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10060451

    authors: Zhang J,Xie W,Yu X,Zhang Z,Zhao Y,Wang N,Wang Y

    更新日期:2019-06-13 00:00:00

  • AMH: Could It Be Used as A Biomarker for Fertility and Superovulation in Domestic Animals?

    abstract::Anti-Müllerian hormone (AMH) is a reliable and easily detectable reproductive marker for the fertility competence of many farm animal species. AMH is also a good predictor of superovulation in cattle, sheep, and mares. In this review, we have summarized the recent findings related to AMH and its predictive reliability...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes10121009

    authors: Umer S,Zhao SJ,Sammad A,Weldegebriall Sahlu B,Yunwei P,Zhu H

    更新日期:2019-12-04 00:00:00

  • Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.).

    abstract::Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus, genome-wide identificatio...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes9030168

    authors: Liu P,Zhang C,Ma JQ,Zhang LY,Yang B,Tang XY,Huang L,Zhou XT,Lu K,Li JN

    更新日期:2018-03-16 00:00:00

  • Aberrant Single Exon Skipping is not Altered by Age in Exons of NF1, RABAC1, AATF or PCGF2 in Human Blood Cells and Fibroblasts.

    abstract::In human pre-mRNA splicing, infrequent errors occur resulting in erroneous splice products as shown in a genome-wide approach. One characteristic subgroup consists of products lacking one cassette exon. The noise in the splicing process, represented by those misspliced products, can be increased by cold shock treatmen...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes2030562

    authors: Mellert K,Uhl M,Högel J,Lamla M,Kemkemer R,Kaufmann D

    更新日期:2011-08-02 00:00:00

  • A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data.

    abstract::Single-cell RNA sequencing (scRNA-seq) has recently brought new insight into cell differentiation processes and functional variation in cell subtypes from homogeneous cell populations. A lack of prior knowledge makes unsupervised machine learning methods, such as clustering, suitable for analyzing scRNA-seq . However,...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10020098

    authors: Zhu X,Li HD,Xu Y,Guo L,Wu FX,Duan G,Wang J

    更新日期:2019-01-29 00:00:00