scholarly journals F5N : Nanopore Sequence Analysis Toolkit for Android Smartphones

2020 ◽  
Author(s):  
Hiruna Samarakoon ◽  
Sanoj Punchihewa ◽  
Anjana Senanayake ◽  
Roshan Ragel ◽  
Hasindu Gamaarachchi
Keyword(s):  
Sequence Analysis ◽  
Mobile Phone ◽  
High Speed ◽  
Sequence Data ◽  
Android Application ◽  
Data Manipulation ◽  
Link Type ◽  
The Cost ◽  
Google Play ◽  
Nanopore Sequencer

AbstractF5N is the first ever Android application for nanopore sequence analysis on a mobile phone, comprised of popular tools for read alignment (Minimap2), sequence data manipulation (Samtools) and methylation calling (F5C/Nanopolish). On NA12878 nanopore data, F5N can perform a complete methylation calling pipeline on a mobile phone in ∼15 minutes for a batch of 4000 nanopore reads (∼34 megabases). F5N is not only a toolkit but also a framework for integrating existing C/C++ based command line tools to run on Android. F5N will enable performing nanopore sequence analysis on-site when used with an ultra-portable nanopore sequencer (eg: MinION or the anticipated smidgION), consequently reducing the cost for special computers and high-speed Internet.Availability and implementationF5N Android application is available on Google Play store at https://play.google.com/store/apps/details?id=com.mobilegenomics.genopo&hl=en and the source code is available on Github at https://github.com/SanojPunchihewa/[email protected]

scholarly journals Comparative Sequence Analysis of Human Minisatellites Showing Meiotic Repeat Instability

1999 ◽  
Vol 9 (2) ◽  
pp. 130-136 ◽  
Author(s):  
John Murray ◽  
Jérôme Buard ◽  
David L. Neil ◽  
Edouard Yeramian ◽  
Keiji Tamaki ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Comparative Sequence Analysis ◽  
Gene Promoters ◽  
Repeat Instability ◽  
Repeat Array ◽  
Comparative Sequence ◽  
Link Type ◽  
Genomic Environment ◽  
Data Library

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF048727(CEB1), AF048728 (MS31A), and AF048729 (MS32).]

ANALISA PERBANDINGAN DALAM RANGKA PEMILIHAN BEBERAPA IP UPSTREAM PROVIDER DI PT. INDOSAT

2018 ◽  
Vol 4 (1) ◽  
pp. 57
Author(s):  
Yuli Anwar ◽  
Dahlar .
Keyword(s):  
Business Strategy ◽  
High Speed ◽  
Human Life ◽  
Sustainable Growth ◽  
The Internet ◽  
Network Service Provider ◽  
High Speed Data ◽  
Telecommunications Services ◽  
The Cost ◽  
Internet Network

Abstract. One of the advances in information technology that now has changed the outlook and human life, business process and business strategy of an institution is the internet. The internet is a very large networks that connected to computers and serves throughout the world in one centralized network. With the internet we can access data and information anytime and anywhere.    As one provider of high-speed data communications services and the pioneer of the internet network service provider in Indonesia that provides integrated services, as well as one of the pioneer development of internet services that provide extensive services in the building and apply it throughout Indonesia. Indosat ready to seize opportunities for sustainable growth of business spectrum are still sprawling Indonesia.    Therefore, Indosat continues to focus on the development of increased efforts to provide the best service for customers of Indosat. Indosat will continue to develop and expand network coverage and a larger investment that the company will achieve excellence in the field of integrated telecommunications services.    Ranking by region of the IP Providers can be seen by grouping IP Providers, and management over IP Providers prefer to choose providers based on where it orginates as an example for the region of the U.S if it will be preferred providers that come from U.S. providers.With the commencement of the internet network optimization start early in 2008 with the selection of the appropriate IP Upstream Provider criteria, it is up to date according to data obtained from Indosat, seen any significant changes to the cost of purchasing capacity of the IP Upstream.    Based on the data obtained that until Q3 or September 2008, the number of IP Upstream Providers that previously there were 20 to 10 IP Upstream Provider, IP Transit Price total decrease of 11% to the price of IP Transit Price / Mbps there is a decrease of 78%, while from the capacity bandwith an increase of 301% capacity from 2008.

Design of Electrolytic Strengthening Machine for Cutting Edge of Cutter

2016 ◽  
Vol 693 ◽  
pp. 1585-1590
Author(s):  
Yi Zhuo Guo ◽  
Xian Guo Yan ◽  
Shu Juan Li ◽  
Hong Guo
Keyword(s):  
Service Life ◽  
Calculation Method ◽  
High Speed ◽  
High Speed Steel ◽  
Cutting Edge ◽  
The Cost ◽  
Electric Quantity

Many studies have proved the service life of cutter can be prolonged by electrolytic strengthening. Based on the theory of electrolytic strengthening technology, this paper introduced and developed prototype equipment for strengthening cutting edge of rotary cutter and put forward a calculation method of total electric quantity consumption during the electrolysis suitable for microcontroller. The M8 high-speed steel tap is taken as a strengthening example. After finished the strengthening process that it clearly see the results of the surface of tap was obviously polished by observing the micrograph. This equipment improves the reliability of electrolytic strengthening and the cost is relatively cheap.

scholarly journals CFD Simulation of a Hyperloop Capsule Inside a Low-Pressure Environment Using an Aerodynamic Compressor as Propulsion and Drag Reduction Method

2021 ◽  
Vol 11 (9) ◽  
pp. 3934
Author(s):  
Federico Lluesma-Rodríguez ◽  
Temoatzin González ◽  
Sergio Hoyas
Keyword(s):  
Shock Waves ◽  
Power Consumption ◽  
High Speed ◽  
Cfd Simulation ◽  
Aerodynamic Drag ◽  
Flow Behavior ◽  
Critical Conditions ◽  
Vehicle Speed ◽  
Blockage Ratio ◽  
The Cost

One of the most restrictive conditions in ground transportation at high speeds is aerodynamic drag. This is even more problematic when running inside a tunnel, where compressible phenomena such as wave propagation, shock waves, or flow blocking can happen. Considering Evacuated-Tube Trains (ETTs) or hyperloops, these effects appear during the whole route, as they always operate in a closed environment. Then, one of the concerns is the size of the tunnel, as it directly affects the cost of the infrastructure. When the tube size decreases with a constant section of the vehicle, the power consumption increases exponentially, as the Kantrowitz limit is surpassed. This can be mitigated when adding a compressor to the vehicle as a means of propulsion. The turbomachinery increases the pressure of part of the air faced by the vehicle, thus delaying the critical conditions on surrounding flow. With tunnels using a blockage ratio of 0.5 or higher, the reported reduction in the power consumption is 70%. Additionally, the induced pressure in front of the capsule became a negligible effect. The analysis of the flow shows that the compressor can remove the shock waves downstream and thus allows operation above the Kantrowitz limit. Actually, for a vehicle speed of 700 km/h, the case without a compressor reaches critical conditions at a blockage ratio of 0.18, which is a tunnel even smaller than those used for High-Speed Rails (0.23). When aerodynamic propulsion is used, sonic Mach numbers are reached above a blockage ratio of 0.5. A direct effect is that cases with turbomachinery can operate in tunnels with blockage ratios even 2.8 times higher than the non-compressor cases, enabling a considerable reduction in the size of the tunnel without affecting the performance. This work, after conducting bibliographic research, presents the geometry, mesh, and setup. Later, results for the flow without compressor are shown. Finally, it is discussed how the addition of the compressor improves the flow behavior and power consumption of the case.

scholarly journals Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

2021 ◽  
Vol 19 (2) ◽  
pp. 769-785 ◽  
Author(s):  
Erwan Sallard ◽  
José Halloy ◽  
Didier Casane ◽  
Etienne Decroly ◽  
Jacques van Helden
Keyword(s):  
Sequence Analysis ◽  
Structure Function ◽  
Molecular Mechanisms ◽  
Laboratory Strain ◽  
Domestic Animals ◽  
Scientific Policy ◽  
Human Coronavirus ◽  
Viral Dissemination ◽  
Link Type ◽  
Intensive Breeding

AbstractSARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure–function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin—natural or synthetic—of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

scholarly journals Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry

2003 ◽  
Vol 93 (2) ◽  
pp. 219-228 ◽  
Author(s):  
Béatrice Denoyes-Rothan ◽  
Guy Guérin ◽  
Christophe Délye ◽  
Barbara Smith ◽  
Dror Minz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Its2 Sequence ◽  
Host Specialization ◽  
Pathogenicity Tests ◽  
Colletotrichum Spp ◽  
Rapd Polymorphism ◽  
Pathogenic Variability

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

Analysis of the Permanent Magnet Guideway of High Temperature Superconducting Maglev

2013 ◽  
Vol 745-746 ◽  
pp. 197-202 ◽  
Author(s):  
Chang Qing Ye ◽  
Zi Gang Deng ◽  
Jia Su Wang
Keyword(s):  
High Temperature ◽  
Permanent Magnet ◽  
High Speed ◽  
Optimization Design ◽  
Optimization Methods ◽  
High Temperature Superconducting ◽  
Practical Engineering ◽  
Hts Maglev ◽  
Ndfeb Permanent Magnet ◽  
The Cost

t was theoretically and experimentally proved that High Temperature Superconducting (HTS) Maglev had huge potential employment in rail transportation and high speed launch system. This had attracted great research interests in practical engineering. The optimization design was one of the most important works in the application of the HTS Maglev. As the NdFeB permanent magnet and HTS materials prices increased constantly, the design optimization of the permanent guideway (PMG) of HTS maglev became one of the indispensable works to decrease the cost of the application. This paper first reviewed four types of PMGs used by the HTS Maglev, then disucssed their structures and magnetic fields. Finally, the optimization methods of these four PMGs were compared. It was suggested that with better optimization methods, the levitation performance within a limit cost got better. That would be helpful to the future numerical optimization of the PMG of the HTS maglev.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

2018 ◽  
Vol 20 (4) ◽  
pp. 1542-1559 ◽  
Author(s):  
Damla Senol Cali ◽  
Jeremie S Kim ◽  
Saugata Ghose ◽  
Can Alkan ◽  
Onur Mutlu
Keyword(s):  
Sequence Analysis ◽  
Genome Assembly ◽  
Sequence Data ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Memory Usage ◽  
Sequencing Technology ◽  
Assembly Pipeline ◽  
And Performance ◽  
Polishing Tool

Abstract Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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