rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output

2021 ◽  
Author(s):  
Marek Schwarz ◽  
Jiří Vohradský ◽  
Josef Pánek
Keyword(s):  
Web Service ◽  
Web Server ◽  
Command Line ◽  
Interactive Analysis ◽  
Blast Output ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Ncbi Blast ◽  
The Web

Abstract Summary We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (HSPs) in BLAST output to their plausible full length, and predicts their homology and secondary structures. The aim of the application is to aid to characterize subject RNAs in HSPs that come uncharacterized in BLAST output. The main advantages of the web-server are easy use and interactive analysis with search, filtering and data export options. Availability and implementation The web server is freely available at rboanalyzer.elixir-czech.cz. The website frontend is implemented in Elm, while backend is implemented in Python and served by Apache.

scholarly journals Long Non-Coding RNA (lncRNA) in Oral Squamous Cell Carcinoma: Biological Function and Clinical Application

Cancers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 5944
Author(s):  
Jianfei Tang ◽  
Xiaodan Fang ◽  
Juan Chen ◽  
Haixia Zhang ◽  
Zhangui Tang
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Molecular Mechanisms ◽  
Non Coding Rna ◽  
Potential Applications ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Oral squamous cell carcinoma (OSCC) is a type of malignancy with high mortality, leading to poor prognosis worldwide. However, the molecular mechanisms underlying OSCC carcinogenesis have not been fully understood. Recently, the discovery and characterization of long non-coding RNAs (lncRNAs) have revealed their regulatory importance in OSCC. Abnormal expression of lncRNAs has been broadly implicated in the initiation and progress of tumors. In this review, we summarize the functions and molecular mechanisms regarding these lncRNAs in OSCC. In addition, we highlight the crosstalk between lncRNA and tumor microenvironment (TME), and discuss the potential applications of lncRNAs as diagnostic and prognostic tools and therapeutic targets in OSCC. Notably, we also discuss lncRNA-targeted therapeutic techniques including CRISPR-Cas9 as well as immune checkpoint therapies to target lncRNA and the PD-1/PD-L1 axis. Therefore, this review presents the future perspectives of lncRNAs in OSCC therapy, but more research is needed to allow the applications of these findings to the clinic.

scholarly journals MyDGR: a server for identification and characterization of diversity-generating retroelements

2019 ◽  
Vol 47 (W1) ◽  
pp. W289-W294 ◽  
Author(s):  
Fatemeh Sharifi ◽  
Yuzhen Ye
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Web Server ◽  
Nucleotide Sequences ◽  
Bacterial Genomes ◽  
Fasta Format ◽  
Reverse Transcriptases ◽  
Identification And Characterization ◽  
The Web

Abstract MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).

scholarly journals Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.

2021 ◽  
Author(s):  
Uciel Chorostecki ◽  
Ester Saus ◽  
Toni Gabaldon
Keyword(s):  
Modular Organization ◽  
Cellular Functions ◽  
Repeat Units ◽  
Non Coding Rna ◽  
High Sequence Conservation ◽  
Non Coding Rnas ◽  
First Time ◽  
Computational Predictions

Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the function of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers of unknown function. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously-unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice

RSC Advances ◽  
2018 ◽  
Vol 8 (60) ◽  
pp. 34408-34417 ◽  
Author(s):  
Wen Qi Li ◽  
Yu Lin Jia ◽  
Feng Quan Liu ◽  
Fang Quan Wang ◽  
Fang Jun Fan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Critical Role ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Epigenetic Regulator ◽  
Non Coding Rnas ◽  
Growth Development ◽  
Long Non Coding Rna ◽  
Identification And Characterization

Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses.

scholarly journals Long non-coding RNA SDCBP2-AS1 delays the progression of ovarian cancer via microRNA-100-5p-targeted EPDR1

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiu Liu ◽  
Chanyuan Liu ◽  
Aijun Zhang ◽  
Qi Wang ◽  
Jiao Ge ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Progression ◽  
Expression Profiling ◽  
Migration And Invasion ◽  
Related Protein ◽  
Biological Functions ◽  
Interactive Analysis ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Abstract Background Dysregulation of long non-coding RNAs has been implied to connect with cancer progression. This research was to decipher the mechanism of long non-coding RNA SDCBP2-AS1 in ovarian cancer (OC) through regulation of microRNA (miR)-100-5p and ependymin-related protein 1 (EPDR1). Methods LncRNA SDCBP2-AS1 and EPDR1 levels in OC were assessed by Gene Expression Profiling Interactive Analysis. lncRNA SDCBP2-AS1, miR-100-5p, and EPDR1 levels in OC tissues and cells were determined. SKOV3 and A2780 cells were transfected with lncRNA SDCBP2-AS1, miR-100-5p, and EPDR1-related plasmids or sequences, and then their functions in cell viability, apoptosis, migration, and invasion were evaluated. The interplay of lncRNA SDCBP2-AS1, miR-100-5p, and EPDR1 was clarified. Results LncRNA SDCBP2-AS1 and EPDR1 levels were suppressed whilst miR-100-5p level was elevated in OC. After upregulating lncRNA SDCBP2-AS1 or EPDR1, viability, migration, and invasion of OC cells were impaired, and apoptosis rate was increased. Downregulating EPDR1 or upregulating miR-100-5p partially mitigated upregulated lncRNA SDCBP2-AS1-induced impacts on the biological functions of OC cells. LncRNA SDCBP2-AS1 sponged miR-100-5p, and EPDR1 was targeted by miR-100-5p. Conclusion It is illustrated that lncRNA SDCBP2-AS1 regulates EPDR1 by sponge adsorption of miR-100-5p to inhibit the progression of OC.

scholarly journals Usage of Web Service in Mobile Application for Parents and Students in Binus School Serpong

2016 ◽  
Vol 7 (3) ◽  
pp. 181
Author(s):  
Karto Iskandar ◽  
Andrew Thejo Putranto
Keyword(s):  
World Wide Web ◽  
Web Services ◽  
Web Service ◽  
Mobile Application ◽  
World Wide ◽  
Electronic Device ◽  
Web Server ◽  
The World ◽  
Data Problem ◽  
The Web

A web service is a service offered by a device electronically to communicate with other electronic device using the World wide web. Smartphone is an electronic device that almost everyone has, especially student and parent for getting information about the school. In BINUS School Serpong mobile application, web services used for getting data from web server like student and menu data. Problem faced by BINUS School Serpong today is the time-consuming application update when using the native application while the application updates are very frequent. To resolve this problem, BINUS School Serpong mobile application will use the web service. This article showed the usage of web services with XML for retrieving data of student. The result from this study is that by using web service, smartphone can retrieve data consistently between multiple platforms. 

scholarly journals Web Service Performance Analysis and Research of Distributed LAMP Architecture

2021 ◽  
Vol 2074 (1) ◽  
pp. 012050
Author(s):  
Yuan Yang
Keyword(s):  
Web Services ◽  
Web Service ◽  
Information Sources ◽  
Early Stage ◽  
Web Server ◽  
Service Performance ◽  
The Internet ◽  
Stage Of Development ◽  
Internet Application ◽  
The Web

Abstract There are many websites on the Internet in the early stage of development, its Web service performance is not strong enough, resulting in the failure to run the system and finally the system crash. Based on this situation, in order to ensure the accurate and efficient service of the Internet website, it is necessary to analyze and study the service performance of the Web. Distributed LAMP architecture studies and analyzes the performance of Web services, which can accurately discover the performance defects and problems of Web, and research a more appropriate configuration of service performance, and the final results presented are more accurate and effective. With the deepening development of the Internet application, the website has become a key window for many people’s information sources. Through the Internet website, we can not only understand the world more comprehensively, but also learn more knowledge. Therefore, building Web services with better performance is something we should consider. In this paper, the performance of the Web server was optimized and improved through the analysis and research of the load of the Web server, and the tuning test was carried out through distributed LAMP architecture by observing the Web service’s access to users, data information maintenance and monitoring, etc.

scholarly journals Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes

2019 ◽  
Vol 21 (2) ◽  
pp. 637-648 ◽  
Author(s):  
Aritro Nath ◽  
Paul Geeleher ◽  
R Stephanie Huang
Keyword(s):  
Expression Patterns ◽  
Imputation Accuracy ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Cancer Tissues ◽  
Long Non Coding Rna

Abstract Long non-coding RNAs (lncRNAs) play an important role in gene regulation and are increasingly being recognized as crucial mediators of disease pathogenesis. However, the vast majority of published transcriptome datasets lack high-quality lncRNA profiles compared to protein-coding genes (PCGs). Here we propose a framework to harnesses the correlative expression patterns between lncRNA and PCGs to impute unknown lncRNA profiles. The lncRNA expression imputation (LEXI) framework enables characterization of lncRNA transcriptome of samples lacking any lncRNA data using only their PCG profiles. We compare various machine learning and missing value imputation algorithms to implement LEXI and demonstrate the feasibility of this approach to impute lncRNA transcriptome of normal and cancer tissues. Additionally, we determine the factors that influence imputation accuracy and provide guidelines for implementing this approach.

Research on Intrusion Detection Method of Web Service Composition

2014 ◽  
Vol 539 ◽  
pp. 331-335
Author(s):  
Xiao Sen Wen
Keyword(s):  
Intrusion Detection ◽  
Web Service ◽  
Service Composition ◽  
Service Providers ◽  
Web Server ◽  
Web Service Composition ◽  
Resource Monitoring ◽  
Detection Model ◽  
The Web ◽  
Standard Service

The paper takes Web service composition document as the research object, through the analysis of the documents, the port and address on the Web server, to create a Web intrusion detection model. The core of the model will monitor the Web server host resources, and finally discusses in detail the design and implementation of resource monitoring system. Intrusion detection model proposed can effectively regulate the behavior of users in this paper, allowing users follow a pre-standard service to call service providers, largely to protect the security of Web services.

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