scholarly journals Inter-chromosomal k-mer distances

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alon Kafri ◽  
Benny Chor ◽  
David Horn
Keyword(s):  
Distance Measures ◽  
Evolutionary Genomics ◽  
Inversion Symmetry ◽  
Bacterial Strains ◽  
Coding Regions ◽  
Reverse Complement ◽  
Synteny Blocks ◽  
Interesting Behavior

Abstract Background Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two k-mer distance measures, D1 and D2, which depend on k. D1 takes into account all k-mers (for a single k) appearing on single strands of the two compared chromosomes, whereas D2 takes into account both strands of each chromosome. Both measures reflect dissimilarities in global chromosomal structures. Results After defining the various distance measures and summarizing their properties, we also define proximities that rely on the existence of synteny blocks between chromosomes of different bacterial strains. Comparing pairs of strains of bacteria, we find negative correlations between synteny proximities and k-mer distances, thus establishing the meaning of the latter as measures of evolutionary distances among bacterial strains. The synteny measures we use are appropriate for closely related bacterial strains, where considerable sections of chromosomes demonstrate high direct or reversed equality. These measures are not appropriate for comparing different bacteria or eukaryotes. K-mer structural distances can be defined for all species. Because of the arbitrariness of strand choices, we employ only the D2 measure when comparing chromosomes of different species. The results for comparisons of various eukaryotes display interesting behavior which is partially consistent with conventional understanding of evolutionary genomics. In particular, we define ratios of minimal k-mer distances (KDR) between unmasked and masked chromosomes of two species, which correlate with both short and long evolutionary scales. Conclusions k-mer distances reflect dissimilarities among global chromosomal structures. They carry information which aggregates all mutations. As such they can complement traditional evolution studies , which mainly concentrate on coding regions.

scholarly journals Inter-chromosomal K-mer Distances

2021 ◽  
Author(s):  
Alon Kafri ◽  
Benny Chor ◽  
David Horn
Keyword(s):  
Distance Measures ◽  
Inversion Symmetry ◽  
The Novel ◽  
Human Chromosomes ◽  
Future Studies ◽  
E Coli ◽  
Human Genomes ◽  
Reverse Complement ◽  
Synteny Blocks ◽  
Different Strains

Abstract BackgroundInversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two distance measures, D1 and D2, where the first takes into account k-mers appearing on single strands of the two chromosomes, whereas the second takes into account both strands.ResultsWe first define the various distance measures and summarize their properties. We also define distances that rely on existence of synteny blocks between chromosomes of different strains. Studying E Coli and Salmonella strains, we evaluate the different distance measures, and find correlations between synteny distances and k-mer distances, thus establishing the usefulness of the latter as measures of evolutional proximity of chromosomes. Applying our measures to human genomes, we find that chromosomes 5 and 6 are the closest ones on the k-mer distance evolutional scale.ConclusionsThe novel distances carry information about evolutional proximity and provide useful tools for future studies. The finding of proximity between human chromosomes 5 and 6 is an examples of a novel insight provided by these tools.

scholarly journals Word Entropy-Based Approach to Detect Highly Variable Genetic Markers for Bacterial Genotyping

2021 ◽  
Vol 12 ◽  
Author(s):  
Marketa Nykrynova ◽  
Vojtech Barton ◽  
Karel Sedlar ◽  
Matej Bezdicek ◽  
Martina Lengerova ◽  
...  
Keyword(s):  
Bacterial Population ◽  
Global Scale ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Bacterial Populations ◽  
Sequence Entropy ◽  
Coding Regions ◽  
Typing Methods ◽  
Multiresistant Strains ◽  
Highly Virulent

Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g., local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also non-coding regions are examined.

scholarly journals Chromosomal Inversion Symmetry: Generalized Chargaff Rules

2015 ◽  
Author(s):  
Sagi Shporer ◽  
Benny Chor ◽  
David Horn
Keyword(s):  
Basic Principle ◽  
Chromosomal Evolution ◽  
Inversion Symmetry ◽  
Statistical Distributions ◽  
Human Chromosomes ◽  
Genomic Evolution ◽  
Chromosomal Structure ◽  
Model Simulations ◽  
Reverse Complement ◽  
Logarithmic Dependence

The generalization of the second Chargaff rule to values of k larger than 1, states that the frequency of any k-mer on a single strand almost equals that of its inverse (reverse-complement). We demonstrate the validity of the generalized rule up to k=10 for all human chromosomes. Moreover, this Inversion Symmetry holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp up to 200 Mbp. We demonstrate that the statistical distributions of inverted pairs of k-mers are very different from other natural pairings of k-mers, implying that inversion symmetry is a basic principle of chromosomal structure. We suggest that it came into being because genomic evolution employed many rearrangements which consisted of inversions of chromosomal sections; on length scales down to order 1-10Kbp. Model simulations substantiate this claim. Low-scale inversions during chromosomal evolution imply that IS may exist for short sections of human chromosomes. This is indeed the case: we find that chromosome sections of length 5Kbp satisfy IS for k=1 and k=2. The largest value of k for which IS holds, which we call the k-limit of IS, increases logarithmically as the section length increases. The logarithmic dependence of the k-limit on the length of the chromosome is a universal characteristic, observed throughout the tree of life.

scholarly journals PaReBrick: PArallel REarrangements and BReakpoints identification toolkit

2021 ◽  
Author(s):  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Olga Bochkareva ◽  
Nikita Alexeev
Keyword(s):  
Antigenic Variation ◽  
Genome Rearrangements ◽  
High Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Phyletic Pattern ◽  
Consistency Results ◽  
Algorithmic Solution ◽  
Synteny Blocks ◽  
Different Strains

Motivation: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation. Specifically, such rearrangements might be responsible for multi-virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results: Here we define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial population, as a tool PaReBrick. The tool takes synteny blocks and a phylogenetic tree as input and outputs rearrangement events. The tool tests each rearrangement for consistency with a tree, and sorts the events by their parallelism score and provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We proved PaReBrick's efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability: PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements .

Sudden generation of anomalous anti-vortex states in a two-component superconductor

2020 ◽  
Vol 34 (31) ◽  
pp. 2050349
Author(s):  
C. A. Aguirre ◽  
Q. D. Martins ◽  
J. Barba-Ortega
Keyword(s):  
Vortex State ◽  
Time Dependent ◽  
Spontaneous Generation ◽  
Cooper Pairs ◽  
Inversion Symmetry ◽  
Ginzburg Landau ◽  
Two Component ◽  
Ginzburg Landau Equations ◽  
Geometrical Defects ◽  
Interesting Behavior

We studied the influences of the inclusion of different geometrical defects (circle, triangle, and square) with different Ginzburg–Landau parameters [Formula: see text] on the vortex state of a mesoscopic superconducting square immersed in an external applied magnetic field. We calculated the magnetization, vorticity, and density of Cooper pairs for this system, solving the time-dependent Ginzburg–Landau equations. We found a novel and interesting behavior of the vorticity [Formula: see text] at low magnetic fields: a spontaneous generation of anti-vortices due to the breaking inversion symmetry.

Determination of the lattice translation across {110} APBs in GaAs

1988 ◽  
Vol 46 ◽  
pp. 600-601
Author(s):  
D.R. Rasmussen ◽  
N.-H. Cho ◽  
C.B. Carter
Keyword(s):  
Grain Boundaries ◽  
Lower Energy ◽  
Antiphase Boundary ◽  
The Other ◽  
Boundary Structure ◽  
Interface Plane ◽  
Inversion Symmetry ◽  
High Angle ◽  
Equilibrium Distance

Domains in GaAs can exist which are related to one another by the inversion symmetry, i.e., the sites of gallium and arsenic in one domain are interchanged in the other domain. The boundary between these two different domains is known as an antiphase boundary [1], In the terminology used to describe grain boundaries, the grains on either side of this boundary can be regarded as being Σ=1-related. For the {110} interface plane, in particular, there are equal numbers of GaGa and As-As anti-site bonds across the interface. The equilibrium distance between two atoms of the same kind crossing the boundary is expected to be different from the length of normal GaAs bonds in the bulk. Therefore, the relative position of each grain on either side of an APB may be translated such that the boundary can have a lower energy situation. This translation does not affect the perfect Σ=1 coincidence site relationship. Such a lattice translation is expected for all high-angle grain boundaries as a way of relaxation of the boundary structure.

SYNTHESIS, CHARACTERIZATION AND BIOLOGICAL EVALUATION OF 3-FORMYL INDOLE BASED SCHIFF BASES

2018 ◽  
Vol 7 (6) ◽  
Author(s):  
Singh Gurvinder ◽  
Singh Prabhsimran ◽  
Dhawan R. K.
Keyword(s):  
Antimicrobial Activity ◽  
Spectral Analysis ◽  
Schiff Bases ◽  
Antimicrobial Agents ◽  
Biological Evaluation ◽  
Fungal Strain ◽  
Bacterial Strains ◽  
Standard Drug ◽  
Gram Negative ◽  
E Coli

In order to develop new antimicrobial agents, a series of 3-formyl indole based Schiff bases were synthesized by reacting 3-formyl indole(indole-3-carboxaldehyde) with substituted aniline taking ethanol as solvent. The reaction was carried in the presence of small amount of p-toluene sulphonic acid as catalyst.All the synthesized compounds were characterized by IR, 1H-NMR spectral analysis. All the synthesized compounds were evaluated for antimicrobial activity against two gram positive bacterial strains (B. subtilisand S. aureus) and two gram negative bacterial strains (P. aeruginosaand E. coli) and one fungal strain (C. albicans). All the synthesized compounds were found to have moderate to good antimicrobial activity. The  standard drug amoxicillin, fluconazole were used for antimicrobial activity. Among the synthesized compounds, the maximum antimicrobial activity was shown by compounds GS04, GS07, GS08 and GS10.

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