scholarly journals VIRMOTIF: A User-Friendly Tool for Viral Sequence Analysis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 186
Author(s):  
Pedram Rajaei ◽  
Khadijeh Hoda Jahanian ◽  
Amin Beheshti ◽  
Shahab S. Band ◽  
Abdollah Dehzangi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Mean Shift ◽  
Virus Genome ◽  
Viral Sequence ◽  
The Past ◽  
Performance Diagnosis ◽  
Wide Range ◽  
Clustering Data ◽  
User Friendly ◽  
Tools And Methods

Bioinformatics and computational biology have significantly contributed to the generation of vast and important knowledge that can lead to great improvements and advancements in biology and its related fields. Over the past three decades, a wide range of tools and methods have been developed and proposed to enhance performance, diagnosis, and throughput while maintaining feasibility and convenience for users. Here, we propose a new user-friendly comprehensive tool called VIRMOTIF to analyze DNA sequences. VIRMOTIF brings different tools together as one package so that users can perform their analysis as a whole and in one place. VIRMOTIF is able to complete different tasks, including computing the number or probability of motifs appearing in DNA sequences, visualizing data using the matplotlib and heatmap libraries, and clustering data using four different methods, namely K-means, PCA, Mean Shift, and ClusterMap. VIRMOTIF is the only tool with the ability to analyze genomic motifs based on their frequency and representation (D-ratio) in a virus genome.

scholarly journals hTFtarget: a comprehensive database for regulations of human transcription factors and their targets

2019 ◽  
Author(s):  
Qiong Zhang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Gene Expression Regulation ◽  
Epigenetic Modification ◽  
Wide Range ◽  
Chromatin Immunoprecipitation Sequencing ◽  
User Friendly

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of Chromatin immunoprecipitation sequencing (ChIP-Seq) provides great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7,190 ChIP-Seq samples of 659 TFs and high confident TF binding sites of 699 TFs) and epigenetic modification information to predict accurate TF-target regulations. hTFtarget offers the following functions for users to explore TF-target regulations: 1) Browse or search general targets of a query TF across datasets; 2) Browse TF-target regulations for a query TF in a specific dataset or tissue; 3) Search potential TFs for a given target gene or ncRNA; 4) Investigate co-association between TFs in cell lines; 5) Explore potential co-regulations for given target genes or TFs; 6) Predict candidate TFBSs on given DNA sequences; 7) View ChIP-Seq peaks for different TFs and conditions in genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF-target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.

i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome

2019 ◽  
Vol 35 (16) ◽  
pp. 2796-2800 ◽  
Author(s):  
Wei Chen ◽  
Hao Lv ◽  
Fulei Nie ◽  
Hao Lin
Keyword(s):  
Dna Sequences ◽  
Rice Genome ◽  
Chemical Properties ◽  
Computational Method ◽  
Accurate Identification ◽  
Feature Selection Technique ◽  
Jackknife Test ◽  
Genome Wide ◽  
Wide Range ◽  
User Friendly

Abstract Motivation DNA N6-methyladenine (6mA) is associated with a wide range of biological processes. Since the distribution of 6mA site in the genome is non-random, accurate identification of 6mA sites is crucial for understanding its biological functions. Although experimental methods have been proposed for this regard, they are still cost-ineffective for detecting 6mA site in genome-wide scope. Therefore, it is desirable to develop computational methods to facilitate the identification of 6mA site. Results In this study, a computational method called i6mA-Pred was developed to identify 6mA sites in the rice genome, in which the optimal nucleotide chemical properties obtained by the using feature selection technique were used to encode the DNA sequences. It was observed that the i6mA-Pred yielded an accuracy of 83.13% in the jackknife test. Meanwhile, the performance of i6mA-Pred was also superior to other methods. Availability and implementation A user-friendly web-server, i6mA-Pred is freely accessible at http://lin-group.cn/server/i6mA-Pred.

A User-Friendly Building Energy Consumption Program

2013 ◽  
Vol 347-350 ◽  
pp. 2642-2646
Author(s):  
Yi Long Jia ◽  
Jian Xiang Jin ◽  
Xuan Hao Zhou
Keyword(s):  
Energy Consumption ◽  
North China ◽  
Building Energy ◽  
Energy Simulation ◽  
Simulation Program ◽  
Building Energy Simulation ◽  
The Past ◽  
Wide Range ◽  
User Friendly ◽  
Easy Operation

Building energy simulation program plays an important role in reducing energy consumption for heating in North China. For the past 60 years, a wide range of building energy simulation programs have been developed. However, in China, building energy simulation programs are not popularized smoothly because of the problems such as unfriendly interface, complex usage and excessively specialized. This paper presents a new building energy simulation program with B/S structure. As a collection of building energy simulation and economic analysis, this program can be accepted by the professionals and non-professionals due to its accuracy and easy operation.

The Functional Psychoses – Are Oncogenes Involved in Their Pathogenesis? Some Speculations

1991 ◽  
Vol 158 (4) ◽  
pp. 563-568 ◽  
Author(s):  
John Leach
Keyword(s):  
Tissue Culture ◽  
Dna Sequences ◽  
Complementary Dna ◽  
Viral Oncogenes ◽  
The Past ◽  
Wide Range ◽  
Functional Psychoses ◽  
Neoplastic Change ◽  
Eukaryotic Organisms

Oncogenes are genes whose expression has been associated with malignant transformation of cells in tissue culture and with neoplastic change in vivo (Bishop, 1987). Much of the current understanding of their nature and action has stemmed from work, over the past 20 years, on tumour viruses (Temin, 1971; Rapp, 1983). One group of tumour viruses, the retroviruses, are unique in possessing an enzyme, reverse transcriptase, which transcribes to the cell DNA a copy of the viral RNA genome (Marks, 1987). After the discovery of viral oncogenes, such DNA copies were used as probes in hybridisation studies (Stehelin et al, 1976; Frankel & Fischinger, 1976). These probes, capable of annealing to complementary DNA sequences, revealed the existence of the latter in normal, unaffected cells (Willecke & Schäfer, 1984). These sequences, called cellular or proto-oncogenes, exist in a wide range of eukaryotic organisms, from yeast to man.

Optical Properties of HVEM Accelerators

1975 ◽  
Vol 33 ◽  
pp. 180-181
Author(s):  
A. Strojnik ◽  
J.W. Scholl ◽  
V. Bevc
Keyword(s):  
Optical Properties ◽  
Electron Accelerator ◽  
Systematic Investigation ◽  
Electron Source ◽  
High Brightness ◽  
The Past ◽  
Wide Range ◽  
Optical Behavior

The electron accelerator, as inserted between the electron source (injector) and the imaging column of the HVEM, is usually a strong lens and should be optimized in order to ensure high brightness over a wide range of accelerating voltages and illuminating conditions. This is especially true in the case of the STEM where the brightness directly determines the highest resolution attainable. In the past, the optical behavior of accelerators was usually determined for a particular configuration. During the development of the accelerator for the Arizona 1 MEV STEM, systematic investigation was made of the major optical properties for a variety of electrode configurations, number of stages N, accelerating voltages, 1 and 10 MEV, and a range of injection voltages ϕ0 = 1, 3, 10, 30, 100, 300 kV).

Pursuit of the Abscopal Effect

2020 ◽  
Vol 04 (04) ◽  
pp. 369-372
Author(s):  
Paul B. Romesser ◽  
Christopher H. Crane
Keyword(s):  
Tumor Immunology ◽  
Antitumor Immunity ◽  
Clinical Success ◽  
Immune Recognition ◽  
Immune Modulators ◽  
Cancer Subtypes ◽  
The Past ◽  
Tumor Irradiation ◽  
Wide Range ◽  
Tumor Recognition

AbstractEvasion of immune recognition is a hallmark of cancer that facilitates tumorigenesis, maintenance, and progression. Systemic immune activation can incite tumor recognition and stimulate potent antitumor responses. While the concept of antitumor immunity is not new, there is renewed interest in tumor immunology given the clinical success of immune modulators in a wide range of cancer subtypes over the past decade. One particularly interesting, yet exceedingly rare phenomenon, is the abscopal response, characterized by a potent systemic antitumor response following localized tumor irradiation presumably attributed to reactivation of antitumor immunity.

The Many Pasts of Detective Fiction

2020 ◽  
Vol 1 (2) ◽  
pp. 157-172
Author(s):  
Thomas Leitch
Keyword(s):  
Detective Fiction ◽  
Golden Age ◽  
Public History ◽  
Detective Novel ◽  
Sherlock Holmes ◽  
Detective Story ◽  
The Past ◽  
Wide Range ◽  
Detective Novels ◽  
The Many

Building on Tzvetan Todorov's observation that the detective novel ‘contains not one but two stories: the story of the crime and the story of the investigation’, this essay argues that detective novels display a remarkably wide range of attitudes toward the several pasts they represent: the pasts of the crime, the community, the criminal, the detective, and public history. It traces a series of defining shifts in these attitudes through the evolution of five distinct subgenres of detective fiction: exploits of a Great Detective like Sherlock Holmes, Golden Age whodunits that pose as intellectual puzzles to be solved, hardboiled stories that invoke a distant past that the present both breaks with and echoes, police procedurals that unfold in an indefinitely extended present, and historical mysteries that nostalgically fetishize the past. It concludes with a brief consideration of genre readers’ own ambivalent phenomenological investment in the past, present, and future each detective story projects.

Nine Centuries of Man

2017 ◽  
Keyword(s):  
Twentieth Century ◽  
Diverse Range ◽  
Gender Expectations ◽  
Court Records ◽  
The Past ◽  
Wide Range ◽  
Police Reports ◽  
Late Twentieth ◽  
Scottish History ◽  
Late Twentieth Century

What did it mean to be a man in Scotland over the past nine centuries? Scotland, with its stereotypes of the kilted warrior and the industrial ‘hard man’, has long been characterised in masculine terms, but there has been little historical exploration of masculinity in a wider context. This interdisciplinary collection examines a diverse range of the multiple and changing forms of masculinities from the late eleventh to the late twentieth century, exploring the ways in which Scottish society through the ages defined expectations for men and their behaviour. How men reacted to those expectations is examined through sources such as documentary materials, medieval seals, romances, poetry, begging letters, police reports and court records, charity records, oral histories and personal correspondence. Focusing upon the wide range of activities and roles undertaken by men – work, fatherhood and play, violence and war, sex and commerce – the book also illustrates the range of masculinities that affected or were internalised by men. Together, the chapters illustrate some of the ways Scotland’s gender expectations have changed over the centuries and how, more generally, masculinities have informed the path of Scottish history

Free but fragile: Human relations amidst poverty and HIV in democratic South Africa

2015 ◽  
Vol 2 (2) ◽  
pp. 85-94
Author(s):  
Christina Landman
Keyword(s):  
South Africa ◽  
Predominantly White ◽  
Black People ◽  
Hiv Treatment ◽  
Human Relations ◽  
White People ◽  
Black And White ◽  
The Past ◽  
Wide Range ◽  
Black Township

Dullstroom-Emnotweni is the highest town in South Africa. Cold and misty, it is situated in the eastern Highveld, halfway between the capital Pretoria/Tswane and the Mozambique border. Alongside the main road of the white town, 27 restaurants provide entertainment to tourists on their way to Mozambique or the Kruger National Park. The inhabitants of the black township, Sakhelwe, are remnants of the Southern Ndebele who have lost their land a century ago in wars against the whites. They are mainly dependent on employment as cleaners and waitresses in the still predominantly white town. Three white people from the white town and three black people from the township have been interviewed on their views whether democracy has brought changes to this society during the past 20 years. Answers cover a wide range of views. Gratitude is expressed that women are now safer and HIV treatment available. However, unemployment and poverty persist in a community that nevertheless shows resilience and feeds on hope. While the first part of this article relates the interviews, the final part identifies from them the discourses that keep the black and white communities from forming a group identity that is based on equality and human dignity as the values of democracy.

FROM THE HISTORY OF THE FORMATION AND DEVELOPMENT OF PERIODICALS IN NAMANGAN

2019 ◽  
Vol 20 (2) ◽  
pp. 49-54
Author(s):  
Dildora Alinazarova ◽  
Keyword(s):  
The Past ◽  
Wide Range ◽  
History Of ◽  
Printing House

In this article, based on an analysis of a wide range of sources, discusses the emergence and development of periodicals and printing house in Namangan. The activities of Ibrat- as the founder of the first printing house in Namangan are considered. In addition, it describes the functioning and development of "Matbaai Ishokia" in the past and present

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