scholarly journals 4SpecID: Reference DNA Libraries Auditing and Annotation System for Forensic Applications

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 61
Author(s):  
Luís Neto ◽  
Nádia Pinto ◽  
Alberto Proença ◽  
António Amorim ◽  
Eduardo Conde-Sousa
Keyword(s):  
Dna Sequences ◽  
Forensic Genetics ◽  
Software Tool ◽  
Taxonomic Assignment ◽  
Specific Data ◽  
Annotation System ◽  
Dna Libraries ◽  
Best Execution ◽  
User Friendly

Forensic genetics is a fast-growing field that frequently requires DNA-based taxonomy, namely, when evidence are parts of specimens, often highly processed in food, potions, or ointments. Reference DNA-sequences libraries, such as BOLD or GenBank, are imperative tools for taxonomic assignment, particularly when morphology is inadequate for classification. The auditing and curation of these datasets require reliable mechanisms, preferably with automated data preprocessing. Software tools were developed to grade these datasets considering as primary criterion the number of records, which is not compliant with forensic standards, where the priority is validation from independent sources. Moreover, 4SpecID is an efficient and freely available software tool developed to audit and annotate reference libraries, specifically designed for forensic applications. Its intuitive user-friendly interface virtually accesses any database and includes specific data mining functions tuned for the widespread BOLD repositories. The built tool was evaluated in laptop MacBook and a dual-Xeon server with a large BOLD dataset (Culicidae, 36,115 records), and the best execution time to grade the dataset on the laptop was 0.28 s. Datasets of Bovidae and Felidae families were used to evaluate the quality of the tool and the relevance of independent sources validation.

scholarly journals DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation

2020 ◽  
Author(s):  
Rui Gan ◽  
Fengxia Zhou ◽  
Yu Si ◽  
Han Yang ◽  
Chuangeng Chen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Bacterial Infections ◽  
Software Tool ◽  
High Specificity ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Accurate Identification ◽  
Bacterial Dna ◽  
Intracellular Form ◽  
User Friendly

AbstractSummaryAs an intracellular form of a bacteriophage in the bacterial host genome, a prophage is usually integrated into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). Phage therapy has been widely applied, for example, using phages to kill bacteria to treat pathogenic and resistant bacterial infections. Therefore, it is necessary to develop effective tools for the fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions of bacterial genomes. DBSCAN-SWA runs faster than any previous tool. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%) and PHASTER (82%) for raw DNA sequences. DBSCAN-SWA also provides user-friendly visualizations including a circular prophage viewer and interactive DataTables.Availability and implementationDBSCAN-SWA is implemented in Python3 and is freely available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.

scholarly journals EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

2018 ◽  
Author(s):  
Michael Gruenstaeudl ◽  
Yannick Hartmaring
Keyword(s):  
Dna Barcoding ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Software Tool ◽  
Plant Dna ◽  
Dna Sequence Data ◽  
User Friendly ◽  
Common Plant ◽  
Python Package

AbstractBackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding.MethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called “checklists”) for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled “EMBL2checklists”, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.ResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study.DiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.

Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes

2020 ◽  
Vol 111 (5) ◽  
pp. 486-490
Author(s):  
Manmohan Pandey ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
Prachi Srivastava ◽  
Suman Saroj ◽  
...  
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Web Browser ◽  
Web Based ◽  
Specific Data ◽  
Sequencing Technologies ◽  
Assembly Algorithms ◽  
User Friendly ◽  
Research Domains ◽  
Generation Sequencing

Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

Simulation and Emulation Tools for Fog Computing

2020 ◽  
Vol 13 ◽  
Author(s):  
Simar Preet Singh ◽  
Rajesh Kumar ◽  
Anju Sharma ◽  
S. Raji Reddy ◽  
Priyanka Vashisht
Keyword(s):  
Quality Of Service ◽  
Programming Languages ◽  
Traffic Management ◽  
Fog Computing ◽  
Research Work ◽  
Research Experience ◽  
Computing Paradigm ◽  
Quality Of Service Parameters ◽  
User Friendly

Background: Fog computing paradigm has recently emerged and gained higher attention in present era of Internet of Things. The growth of large number of devices all around, leads to the situation of flow of packets everywhere on the Internet. To overcome this situation and to provide computations at network edge, fog computing is the need of present time that enhances traffic management and avoids critical situations of jam, congestion etc. Methods: For research purposes, there are many methods to implement the scenarios of fog computing i.e. real-time implementation, implementation using emulators, implementation using simulators etc. The present study aims to describe the various simulation and emulation tools for implementing fog computing scenarios. Results: Review shows that iFogSim is the simulator that most of the researchers use in their research work. Among emulators, EmuFog is being used at higher pace than other available emulators. This might be due to ease of implementation and user-friendly nature of these tools and language these tools are based upon. The use of such tools enhance better research experience and leads to improved quality of service parameters (like bandwidth, network, security etc.). Conclusion: There are many fog computing simulators/emulators based on many different platforms that uses different programming languages. The paper concludes that the two main simulation and emulation tools in the area of fog computing are iFogSim and EmuFog. Accessibility of these simulation/emulation tools enhance better research experience and leads to improved quality of service parameters along with the ease of their usage.

scholarly journals DMSO Improves the Ski-Slope Effect in Direct PCR

2021 ◽  
Vol 11 (4) ◽  
pp. 1943
Author(s):  
Joo-Young Kim ◽  
Ju Yeon Jung ◽  
Da-Hye Kim ◽  
Seohyun Moon ◽  
Won-Hae Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Pcr Amplification ◽  
Analytical Techniques ◽  
Direct Pcr ◽  
Dna Profile ◽  
Novel Technologies ◽  
Specific Amplification ◽  
Polymerase Chain ◽  
Dna Profiles

Analytical techniques such as DNA profiling are widely used in various fields, including forensic science, and novel technologies such as direct polymerase chain reaction (PCR) amplification are continuously being developed in order to acquire DNA profiles efficiently. However, non-specific amplification may occur depending on the quality of the crime scene evidence and amplification methods employed. In particular, the ski-slope effect observed in direct PCR amplification has led to inaccurate interpretations of the DNA profile results. In this study, we aimed to reduce the ski-slope effect by using dimethyl sulfoxide (DMSO) in direct PCR. We confirmed that DMSO (3.75%, v/v) increased the amplification yield of large-sized DNA sequences more than that of small-sized ones. Using 50 Korean buccal samples, we further demonstrated that DMSO reduced the ski-slope effect in direct PCR. These results suggest that the experimental method developed in this study is suitable for direct PCR and may help to successfully obtain DNA profiles from various types of evidence at crime scenes.

scholarly journals Techniques for Mitigating the Effects of Smoke Taint While Maintaining Quality in Wine Production: A Review

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1672
Author(s):  
Ysadora A. Mirabelli-Montan ◽  
Matteo Marangon ◽  
Antonio Graça ◽  
Christine M. Mayr Marangon ◽  
Kerry L. Wilkinson
Keyword(s):  
Global Perspective ◽  
Wine Industry ◽  
Wine Production ◽  
Specific Data ◽  
Main Research ◽  
Initial Severity ◽  
The Subject ◽  
Available Information

Smoke taint has become a prominent issue for the global wine industry as climate change continues to impact the length and extremity of fire seasons around the world. Although the issue has prompted a surge in research on the subject in recent years, no singular solution has yet been identified that is capable of maintaining the quality of wine made from smoke-affected grapes. In this review, we summarize the main research on smoke taint, the key discoveries, as well as the prevailing uncertainties. We also examine methods for mitigating smoke taint in the vineyard, in the winery, and post production. We assess the effectiveness of remediation methods (proposed and actual) based on available research. Our findings are in agreement with previous studies, suggesting that the most viable remedies for smoke taint are still the commercially available activated carbon fining and reverse osmosis treatments, but that the quality of the final treated wines is fundamentally dependent on the initial severity of the taint. In this review, suggestions for future studies are introduced for improving our understanding of methods that have thus far only been preliminarily investigated. We select regions that have already been subjected to severe wildfires, and therefore subjected to smoke taint (particularly Australia and California) as a case study to inform other wine-producing countries that will likely be impacted in the future and suggest specific data collection and policy implementation actions that should be taken, even in countries that have not yet been impacted by smoke taint. Ultimately, we streamline the available information on the topic of smoke taint, apply it to a global perspective that considers the various stakeholders involved, and provide a launching point for further research on the topic.

scholarly journals Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Congyu Lu ◽  
Zheng Zhang ◽  
Zena Cai ◽  
Zhaozhong Zhu ◽  
Ye Qiu ◽  
...  
Keyword(s):  
Prediction Accuracy ◽  
Functional Characterization ◽  
Gaussian Model ◽  
Software Tool ◽  
Biological Properties ◽  
Rapid Identification ◽  
Taxonomic Assignment ◽  
Genus Level ◽  
Alignment Free ◽  
Archaeal Viruses

Abstract Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

scholarly journals XRD Data Visualization, Processing and Analysis with d1Dplot and d2Dplot Software Packages

Proceedings ◽  
2020 ◽  
Vol 62 (1) ◽  
pp. 9
Author(s):  
Oriol Vallcorba ◽  
Jordi Rius
Keyword(s):  
Data Analysis ◽  
Data Visualization ◽  
X Ray Diffraction ◽  
Specific Data ◽  
X Ray ◽  
Software Packages ◽  
Compound Database ◽  
Synchrotron Light ◽  
User Friendly ◽  
Transformation Processes

The d1Dplot and d2Dplot computer programs have been developed as user-friendly tools for the inspection and processing of 1D and 2D X-ray diffraction (XRD) data, respectively. d1Dplot provides general tools for data processing and includes the ability to generate comprehensive 2D plots of multiple patterns to easily follow transformation processes. d2Dplot is a full package for 2D XRD data. Besides general processing tools, it includes specific data analysis routines for the application of the through-the-substrate methodology [Rius et al. IUCrJ 2015, 2, 452–463]. Both programs allow the creation of a user compound database for the identification of crystalline phases. The software can be downloaded from the ALBA Synchrotron Light Source website and can be used free of charge for non-commercial and academic purposes.

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

2020 ◽  
Vol 36 (12) ◽  
pp. 3913-3915
Author(s):  
Hemi Luan ◽  
Xingen Jiang ◽  
Fenfen Ji ◽  
Zhangzhang Lan ◽  
Zongwei Cai ◽  
...  
Keyword(s):  
False Positive ◽  
Supplementary Information ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Metabolomics Data ◽  
Web Based ◽  
Tremendous Amount ◽  
Chromatographic Peaks ◽  
User Friendly

Abstract Motivation Liquid chromatography–mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement. Results To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies. Availability and implementation The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva. Supplementary information Supplementary data are available at Bioinformatics online.

An Energy Balanced Ad Hoc Multicast Routing Algorithm

2012 ◽  
Vol 466-467 ◽  
pp. 425-429
Author(s):  
Qi Zhang ◽  
Hai Jun Xiong
Keyword(s):  
Ad Hoc Network ◽  
Ad Hoc ◽  
Multicast Routing ◽  
Routing Algorithm ◽  
Energy Model ◽  
Specific Data ◽  
Routing Technology ◽  
Multicast Routing Algorithm ◽  
Energy Network

Multicast routing technology of Ad hoc network is a method of transferring specific data to a group of clients selectively; therefore, quality of the services is the key to evaluate the method. After the analysis of energy model and other routing algorithms ,an energy model and a balanced energy network multicast routing algorithm EBAMRA have been proposed in this article,. Experiments had been done, the simulation results show that this algorithm is feasible and effective, which provides a new and effective way of Ad hoc multicast routing technology.

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