scholarly journals Nfeature: A platform for computing features of nucleotide sequences

2021 ◽  
Author(s):  
Megha Mathur ◽  
Sumeet Patiyal ◽  
Anjali Dhall ◽  
Shipra Jain ◽  
Ritu Tomer ◽  
...  
Keyword(s):  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Machine Learning Techniques ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Reverse Complement ◽  
Wide Range ◽  
Public Repositories ◽  
Exponential Rates ◽  
And Function

In the past few decades, public repositories on nucleotides have increased with exponential rates. This pose a major challenge to researchers to predict the structure and function of nucleotide sequences. In order to annotate function of nucleotide sequences it is important to compute features/attributes for predicting function of these sequences using machine learning techniques. In last two decades, several software/platforms have been developed to elicit a wide range of features for nucleotide sequences. In order to complement the existing methods, here we present a platform named Nfeature developed for computing wide range of features of DNA and RNA sequences. It comprises of three major modules namely Composition, Correlation, and Binary profiles. Composition module allow to compute different type of compositions that includes mono-/di-tri-nucleotide composition, reverse complement composition, pseudo composition. Correlation module allow to compute various type of correlations that includes auto-correlation, cross-correlation, pseudo-correlation. Similarly, binary profile is developed for computing binary profile based on nucleotides, di-nucleotides, di-/tri-nucleotide properties. Nfeature also allow to compute entropy of sequences, repeats in sequences and distribution of nucleotides in sequences. In addition to compute feature in whole sequence, it also allows to compute features from part of sequence like split-composition, N-terminal, C-terminal. In a nutshell, Nfeature amalgamates existing features as well as number of novel features like nucleotide repeat index, distance distribution, entropy, binary profile, and properties. This tool computes a total of 29217 and 14385 features for DNA and RNA sequence, respectively. In order to provide, a highly efficient and user-friendly tool, we have developed a standalone package and web-based platform (https://webs.iiitd.edu.in/raghava/nfeature).

scholarly journals Scaling and Visualization of Nucleotide Sequences

2019 ◽  
Vol 224 ◽  
pp. 03007
Author(s):  
Ivan V. Stepanyan ◽  
Abbakar M. Khussein
Keyword(s):  
Genetic Information ◽  
Visual Representations ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Coordinate Systems ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Fractal Clusters ◽  
Living Organisms ◽  
Orthogonal Coordinate Systems

Algorithms for scaling and visualization of nucleotide sequences developed in this study allow identifying relationships between the biochemical parameters of DNA and RNA molecules with scale invariance, fractal clusters, nonlinear ordering and symmetry and noise immunity of visual representations in orthogonal coordinate systems. The algorithms are capable of displaying structures of the nucleotide sequences of living organisms by visualizing them in spaces of various dimensions and scales. Approximately one hundred genes (protozoa, plants, fungi, animals, viruses) were analysed and examples of visualization of the nucleotide composition of genomes of various species have been presented. The developed method contributes to an in-depth understanding of the principles of genetic coding and simplifying the perception of genetic information due to the algorithmic interpretation of the basic properties of polynucleotide fragments with visualization of the final geometric structure of the genetic code.

scholarly journals Processing Oxford Nanopore Long Reads Using Amazon Web Services

2020 ◽  
Vol 3 (4) ◽  
pp. e00131
Author(s):  
V.V. Shapovalova ◽  
S.P. Radko ◽  
K.G. Ptitsyn ◽  
G.S. Krasnov ◽  
K.V. Nakhod ◽  
...  
Keyword(s):  
Web Services ◽  
Primary Data ◽  
Rna Sequences ◽  
Computing Power ◽  
Dna And Rna ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Wide Range ◽  
Amazon Web Services ◽  
Selection Of

Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the "Oxford nanopore".

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

Chaperonin as the normal controls and pathological anti-stress response in the human reproductive system

2016 ◽  
pp. 126-129
Author(s):  
M. Makarenko ◽  
◽  
D. Hovsyeyev ◽  
L. Sydoryk ◽  
◽  
...  
Keyword(s):  
Reproductive System ◽  
Stress Proteins ◽  
Physiological Stress ◽  
Protein Complexes ◽  
Reproductive Function ◽  
Intercellular Signaling ◽  
Toll Like Receptors ◽  
Wide Range ◽  
Protein Functions ◽  
And Function

Different kinds of physiological stress cause mass changes in the cells, including the changes in the structure and function of the protein complexes and in separate molecules. The protein functions is determined by its folding (the spatial conclusion), which depends on the functioning of proteins of thermal shock- molecular chaperons (HSPs) or depends on the stress proteins, that are high-conservative; specialized proteins that are responsible for the correct proteinaceous folding. The family of the molecular chaperones/ chaperonins/ Hsp60 has a special place due to the its unique properties of activating the signaling cascades through the system of Toll-like receptors; it also stimulates the cells to produce anti- inflammatory cytokines, defensins, molecules of cell adhesion and the molecules of MHC; it functions as the intercellular signaling molecule. The pathological role of Hsp60 is established in a wide range of illnesses, from diabetes to atherosclerosis, where Hsp60 takes part in the regulation of both apoptosis and the autoimmune processes. The presence of the HSPs was found in different tissues that are related to the reproductive system. Key words: molecular chaperons (HSPs), Toll-like receptors, reproductive function, natural auto antibody.

Possession and Repetition

2012 ◽  
Vol 6 (1-3) ◽  
pp. 243-259 ◽  
Author(s):  
Yohan Yoo
Keyword(s):  
First Century ◽  
Daily Lives ◽  
Modern Times ◽  
Sacred Texts ◽  
New Methods ◽  
Wide Range ◽  
Lay Buddhists ◽  
Iconic Status ◽  
And Function ◽  
To Receive

This article demonstrates the need for the iconic status and function of Buddhist scripture to receive more attention by illuminating how lay Korean Buddhists try to appropriate the power of sutras. The oral and aural aspects of scripture, explained by Wilfred Cantwell Smith, provide only a limited understanding of the characteristics of scripture. It should be noted that, before modern times, most lay people, not only in Buddhist cultures but also in Christian and other traditions, neither had the chance to recite scriptures nor to listen to their recitations regularly. Several clear examples demonstrate contemporary Korean Buddhists’ acceptance of the iconic status of sutras and their attempt to appropriate the power and status of those sacred texts. In contemporary Korea, lay Buddhists try to claim the power of scriptures in their daily lives by repeating and possessing them. Twenty-first century lay believers who cannot read or recite in a traditional style have found new methods of repetition, such as internet programs for copying sacred texts and for playing recordings of their recitations. In addition, many Korean Buddhists consider the act of having sutras in one’s possession to be an effective way of accessing the sacred status and power of these texts. Hence, various ways of possessing them have been developed in a wide range of products, from fancy gilded sutras to sneakers embroidered with mantras.

Efficient Prediction of Structural and Electronic Properties of Hybrid 2D Materials Using DFT and Machine Learning

2018 ◽  
Author(s):  
Sherif Tawfik ◽  
Olexandr Isayev ◽  
Catherine Stampfl ◽  
Joseph Shapter ◽  
David Winkler ◽  
...  
Keyword(s):  
Machine Learning ◽  
Band Gap ◽  
Density Functional ◽  
2D Materials ◽  
Van Der Waals ◽  
Building Blocks ◽  
Machine Learning Techniques ◽  
Interlayer Distance ◽  
Computational Screening ◽  
Wide Range

Materials constructed from different van der Waals two-dimensional (2D) heterostructures offer a wide range of benefits, but these systems have been little studied because of their experimental and computational complextiy, and because of the very large number of possible combinations of 2D building blocks. The simulation of the interface between two different 2D materials is computationally challenging due to the lattice mismatch problem, which sometimes necessitates the creation of very large simulation cells for performing density-functional theory (DFT) calculations. Here we use a combination of DFT, linear regression and machine learning techniques in order to rapidly determine the interlayer distance between two different 2D heterostructures that are stacked in a bilayer heterostructure, as well as the band gap of the bilayer. Our work provides an excellent proof of concept by quickly and accurately predicting a structural property (the interlayer distance) and an electronic property (the band gap) for a large number of hybrid 2D materials. This work paves the way for rapid computational screening of the vast parameter space of van der Waals heterostructures to identify new hybrid materials with useful and interesting properties.

The Art of Love Poetry

2018 ◽  
Author(s):  
Erik Gray
Keyword(s):  
Popular Culture ◽  
Cultural History ◽  
Literary Tradition ◽  
Love Poetry ◽  
Erotic Love ◽  
Wide Range ◽  
History Of ◽  
And Function ◽  
Meaning And Function ◽  
Comprehensive History

Love begets poetry; poetry begets love. These two propositions have seemed evident to thinkers and poets across the Western literary tradition. Plato writes that “anyone that love touches instantly becomes a poet.” And even today, when poetry has largely disappeared from the mainstream of popular culture, it retains its romantic associations. But why should this be so—what are the connections between poetry and erotic love that lead us to associate them so strongly with one another? An examination of different theories of both love and poetry across the centuries reveals that the connection between them is not merely an accident of cultural history—the result of our having grown up hearing, or hearing about, love poetry—but something more intrinsic. Even as definitions of them have changed, the two phenomena have consistently been described in parallel terms. Love is characterized by paradox. Above all, it is both necessarily public, because interpersonal, and intensely private; hence it both requires expression and resists it. In poetry, especially lyric poetry, which features its own characteristic paradoxes and silences, love finds a natural outlet. This study considers both the theories and the love poems themselves, bringing together a wide range of examples from different eras in order to examine the major structures that love and poetry share. It does not aim to be a comprehensive history of Western love poetry, but an investigation into the meaning and function of recurrent tropes, forms, and images employed by poets to express and describe erotic love.

scholarly journals TOWARDS FUNCTIONAL ARCHITECTURAL DECOMPOSITION OF CONSTRAINED LAYER INFLATABLE SYSTEMS

2021 ◽  
Vol 1 ◽  
pp. 3219-3228
Author(s):  
Koray Benli ◽  
Jonathan Luntz ◽  
Diann Brei ◽  
Wonhee Kim ◽  
Paul Alexander ◽  
...  
Keyword(s):  
Conceptual Design ◽  
Form And Function ◽  
New Concepts ◽  
Wide Range ◽  
Systematic Understanding ◽  
And Function

AbstractPneumatically activated systems enable myriad types of highly functional inflatables employing a wide range of architectural approaches affecting their form and function, making systematic conceptual design difficult. A new architectural class of pneumatically activated systems, constrained layer inflatable systems, consists of hierarchically architected flat layers of thin airtight bladders that are internally and/or externally constrained to generate a variety of functionalities. The highly hierarchical architectural structure of constrained layer inflatable systems coincides with the hierarchy of produced functions, providing an opportunity for the development of a functional architectural decomposition, capturing the inherent relationship between architectural and functional hierarchies. The basis of the approach is conveyed through the design of an example constrained layer inflatable system. This approach empowers the systematic understanding of the interrelated architectural and functional breakdown of constrained layer inflatable systems, enabling designers to iteratively analyze, synthesize, and re-synthesize the components of the system improving existing designs and exploring new concepts.

scholarly journals Recent Advances in Unmanned Aerial Vehicle Forest Remote Sensing—A Systematic Review. Part I: A General Framework

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 327 ◽  
Author(s):  
Riccardo Dainelli ◽  
Piero Toscano ◽  
Salvatore Filippo Di Gennaro ◽  
Alessandro Matese
Keyword(s):  
Remote Sensing ◽  
Unmanned Aerial Vehicle ◽  
Relevant Information ◽  
Forest Monitoring ◽  
Machine Learning Techniques ◽  
Planted Forests ◽  
Systematic Analysis ◽  
Aerial Photogrammetry ◽  
Wide Range ◽  
Aerial Vehicle

Natural, semi-natural, and planted forests are a key asset worldwide, providing a broad range of positive externalities. For sustainable forest planning and management, remote sensing (RS) platforms are rapidly going mainstream. In a framework where scientific production is growing exponentially, a systematic analysis of unmanned aerial vehicle (UAV)-based forestry research papers is of paramount importance to understand trends, overlaps and gaps. The present review is organized into two parts (Part I and Part II). Part II inspects specific technical issues regarding the application of UAV-RS in forestry, together with the pros and cons of different UAV solutions and activities where additional effort is needed, such as the technology transfer. Part I systematically analyzes and discusses general aspects of applying UAV in natural, semi-natural and artificial forestry ecosystems in the recent peer-reviewed literature (2018–mid-2020). The specific goals are threefold: (i) create a carefully selected bibliographic dataset that other researchers can draw on for their scientific works; (ii) analyze general and recent trends in RS forest monitoring (iii) reveal gaps in the general research framework where an additional activity is needed. Through double-step filtering of research items found in the Web of Science search engine, the study gathers and analyzes a comprehensive dataset (226 articles). Papers have been categorized into six main topics, and the relevant information has been subsequently extracted. The strong points emerging from this study concern the wide range of topics in the forestry sector and in particular the retrieval of tree inventory parameters often through Digital Aerial Photogrammetry (DAP), RGB sensors, and machine learning techniques. Nevertheless, challenges still exist regarding the promotion of UAV-RS in specific parts of the world, mostly in the tropical and equatorial forests. Much additional research is required for the full exploitation of hyperspectral sensors and for planning long-term monitoring.

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