scholarly journals DNAlogo: a smart mini application for generating DNA sequence logos

2016 ◽  
Author(s):  
Yabin Guo
Keyword(s):  
Developing Countries ◽  
Nucleic Acids ◽  
Dna Sequence ◽  
Sequence Logo ◽  
The Internet ◽  
Graphic Interface ◽  
Consensus Sequences ◽  
Sequence Logos ◽  
Programming Knowledge ◽  
Gc Contents

AbstractSequence logos are frequently used for presenting consensus sequences and motifs of nucleic acids and proteins. WebLogo of UC Berkeley is the most popular tool for creating sequence logos, whereas, it is often restricted by the internet speed in some developing countries and no graphic interface for its stand-alone version. Here, the author generated an application, DNAlogo, using VB.net, which runs in Windows system. DNAlogo is small and convenient. It creates both bitmap and vector map. Beside the classic sequence logo function, DNAlogo introduced compensated logo to generate consensus sequences considering different GC contents of different genomes. DNAlogo provides a simple way for researchers without programming knowledge to create DNA sequence logos.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

scholarly journals Effectiveness of the Internet-based Versus Face-to-Face Interaction on Reduction of Tobacco use among Adults: A Systematic Review and Meta-Analysis

2021 ◽  
Author(s):  
Rajesh Kumar ◽  
Ravi Kant ◽  
Poonam Yadav ◽  
Tamar Rodney ◽  
Mukesh Bairwa
Keyword(s):  
Developing Countries ◽  
Tobacco Use ◽  
Meta Analysis ◽  
Intervention Group ◽  
The Internet ◽  
Control Group ◽  
Forest Plot ◽  
Cochrane Central Register ◽  
Face To Face

Abstract BackgroundThe burden of tobacco-associated disorders is prevalent worldwide. Over the years, many innovative internet-based approaches have been utilized with variable success to quit tobacco. Though the effectiveness of internet-based and face-to-face interventions on quitting smoking are very well reported in the literature, due to limitation in methodology and limited sample size, it is required to integrate and analyze these studies' findings to reach a single conclusion. The study evaluated the effectiveness of the internet as an intervention approach versus face-to-face interaction on reducing tobacco use as control among adults.MethodsA systematic search was performed through various electronic databases such as Medline, PsychInfo, PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), ResearchGate, Google Scholar, and Academia. Reference lists of the eligible articles were also screened. Full-text articles were included as per eligibility criteria (PICO framework). No ethnicity restriction was applied.ResultsA total of 13 studies were selected for meta-analysis, with 3852 and 3908 participants in intervention and control groups respectively. Forest plot favours the intervention group at one month follow up for tobacco quitting (OR: 2.37, CI: 1.86-3.02, P-0.00001, I2 =0%), at three months (OR: 1.88, CI: 1.48-2.40, P-0.00001, I2 =42%) at six months (OR: 2.02, CI: 1.64-2.50, P-0.00001, I2 =38%) and at 1 year of follow-up (OR: 1.43, CI: 1.18-1.74, P-0.00001, I2 = 36%) comparing to control group. ConclusionInternet and web-based interventions are highly useful in tobacco quitting at one month, three months, six months, and one year of follow-up compared to face-to-face interaction or no intervention, although the level of evidence was moderate. Additionally, limited availability of trials in developing countries, arising need for research of internet use in developing countries to quit tobacco. Prospero Registration number- PROSPERO 2020 CRD42020214306

scholarly journals Chasing Ghosts: Rumours and Representations of the Export of Chinese Convict Labour to Developing Countries

2012 ◽  
Vol 210 ◽  
pp. 398-418 ◽  
Author(s):  
Yan Hairong ◽  
Barry Sautman
Keyword(s):  
Developing Countries ◽  
The Internet ◽  
Chinese Government ◽  
Grass Roots ◽  
Local Media ◽  
Chinese Official ◽  
Global Discourse ◽  
Recent Addition ◽  
Political Economic ◽  
Opposition Parties

AbstractA recent addition to the global discourse of China's interaction with developing countries has been the claim that the Chinese government exports prison labour to these countries. While no evidence is ever presented to support this claim, it has been widely circulated in international and local media, as well as on the internet. This article examines the origins of the rumour and the mechanisms of its transmission. It shows that while the rumour often originates at the grass roots in developing countries, it is promoted locally and globally by political, economic and media elites with distinct agendas that often involve building support for opposition parties, competition in obtaining contracts, or geo-strategic and ideological rivalry. We analyse the rumour's circulation in light of the larger discourse on China and developing countries, and discuss why Chinese official responses to the claim have proved to be ineffective.

Policy Perspectives and Strategy for Communication Data and Network Security Projects and Tools

2014 ◽  
pp. 386-399
Author(s):  
Inderjeet Singh Sodhi
Keyword(s):  
Developing Countries ◽  
Network Security ◽  
Computer Network ◽  
The Internet ◽  
Network Systems ◽  
Constant Increase ◽  
Policy And Strategy ◽  
Effective Policy ◽  
The Government ◽  
Increasing Demand

This chapter highlights the constant increase in the number of attacks on computer network systems, which has pushed governments, researchers, and experts to devise better security policies and strategies. However, the rapid growth of systems, components, and services offered has increased the difficulty of administering them. In many organizations in developed and developing countries, more emphasis is being given on use of Automatic Computing for proper network security. The chapter clarifies how various projects and tools could be relevant for network security. The chapter provides insights about what steps have been taken for network security in a developing country like India. It looks into various strategies adopted for communication data and network security in India. It emphasizes that, with increasing demand for basic/citizen services over the Internet, it has become important to protect data and ensure efficient backup and data recovery. The chapter proposes a need for better and effective policy and strategy for communication data and network security to make the government citizen-oriented in developing countries.

E-Government Issues in Developing Countries

2012 ◽  
pp. 423-439
Author(s):  
Gohar Feroz Khan ◽  
Junghoon Moon
Keyword(s):  
Developing Countries ◽  
Mobile Phone ◽  
Digital Divide ◽  
Public Services ◽  
Social Economic ◽  
Developed Countries ◽  
Electronic Government ◽  
The Internet ◽  
Government Agencies ◽  
Government Services

Electronic government, or e-Government, is the practice of providing public services to citizens, businesses, and other government agencies where government services can be accessed through the Internet, mobile phone, fax, mail, telephone, and personal visits (MGAHA, 2005). Developing countries, utilizing the late comer advantage, are mimicking trends of paperless governments with the expectations to reap the same benefits enjoyed by developed countries. However, e-Government initiatives have not always been successful in developing countries. According to the study conducted by Heeks (2003), the rate of e-Government success in developing countries was only 15 percent. The authors believe that such failures are mainly due to certain unique social, economic, technological, and environmental challenges faced by e-Government in developing countries. For example, some major issues include digital divide, political instability, and skills-related issues. However, the research dealing with these problems is limited. Therefore, in this chapter, the authors discuss these challenges.

The Elusive Last Mile to the Internet

2011 ◽  
pp. 540-560
Author(s):  
V. Sridhar ◽  
Piyush Jain
Keyword(s):  
Developing Countries ◽  
Information Systems ◽  
High Speed ◽  
Service Providers ◽  
Internet Access ◽  
Service Level ◽  
The Internet ◽  
Service Level Agreements ◽  
Last Mile ◽  
Mission Critical

This case highlights the challenges faced by organizations in developing countries in getting reliable, high-speed Internet access to support their mission critical web enabled information systems. The case prescribes various measures to optimally use the constrained bandwidth available from service providers. The challenges in defining and monitoring appropriate service level agreements with the service providers are discussed.

The Changing World of ICT and Health

2011 ◽  
pp. 111-128
Author(s):  
Prajesh Chhanabhai ◽  
Alec Holt
Keyword(s):  
Developing Countries ◽  
Health Information ◽  
Mobile Phones ◽  
Communication Technology ◽  
Rapid Change ◽  
Healthcare Sector ◽  
The Internet ◽  
Communication Techniques ◽  
Health Consumer ◽  
Information And Communication

Information and Communication Technology (ICT) has undergone rapid change in the last decade and it is now readily accessible within many communities. This change has resulted in a revolution in the healthcare sector as technology has steadily empowered the health consumer. However, the problem of the digital divide remains and may be widening with the growth of technology. This chapter will examine how developing countries have overcome this problem by using varying communication techniques to share health information. The chapter also suggests how mobile phones can provide a more accessible conduit for sharing health information in developing countries as opposed to the Internet alone. These changes need to be embraced in order to provide a framework that will allow ICT to narrow, rather than widen the gap between the information poor and the information rich.

scholarly journals Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 353-358
Author(s):  
Mengchi Wang ◽  
David Wang ◽  
Kai Zhang ◽  
Vu Ngo ◽  
Shicai Fan ◽  
...  
Keyword(s):  
Binding Sites ◽  
Information Loss ◽  
Mathematical Framework ◽  
Consensus Sequences ◽  
Statistical Justification ◽  
Sequence Logos ◽  
Precision Recall Curve ◽  
Positional Weight ◽  
Jensen Shannon Divergence ◽  
Motif Information

Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus sequences. We name this representation as sequence Motto and have implemented an efficient algorithm with flexible options for converting motif PWMs into Motto from nucleotides, amino acids, and customized characters. We show that this representation provides a simple and efficient way to identify the binding sites of 1156 common transcription factors (TFs) in the human genome. The effectiveness of the method was benchmarked by comparing sequence matches found by Motto with PWM scanning results found by FIMO. On average, our method achieves a 0.81 area under the precision-recall curve, significantly (P-value < 0.01) outperforming all existing methods, including maximal positional weight, Cavener’s method, and minimal mean square error. We believe this representation provides a distilled summary of a motif, as well as the statistical justification.

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