scholarly journals m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human

2020 ◽  
Vol 36 (11) ◽  
pp. 3528-3536 ◽  
Author(s):  
Bowen Song ◽  
Yujiao Tang ◽  
Kunqi Chen ◽  
Zhen Wei ◽  
Rong Rong ◽  
...  
Keyword(s):  
Recent Progress ◽  
Web Server ◽  
High Accuracy ◽  
Supplementary Information ◽  
Genetic Mutations ◽  
Supplementary Data ◽  
Rna Methylation ◽  
Online Platform ◽  
Main Components ◽  
The Impact

Abstract Motivation Recent progress in N7-methylguanosine (m7G) RNA methylation studies has focused on its internal (rather than capped) presence within mRNAs. Tens of thousands of internal mRNA m7G sites have been identified within mammalian transcriptomes, and a single resource to best share, annotate and analyze the massive m7G data generated recently are sorely needed. Results We report here m7GHub, a comprehensive online platform for deciphering the location, regulation and pathogenesis of internal mRNA m7G. The m7GHub consists of four main components, including: the first internal mRNA m7G database containing 44 058 experimentally validated internal mRNA m7G sites, a sequence-based high-accuracy predictor, the first web server for assessing the impact of mutations on m7G status, and the first database recording 1218 disease-associated genetic mutations that may function through regulation of m7G methylation. Together, m7GHub will serve as a useful resource for research on internal mRNA m7G modification. Availability and implementation m7GHub is freely accessible online at www.xjtlu.edu.cn/biologicalsciences/m7ghub. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19

2020 ◽  
Vol 36 (20) ◽  
pp. 5109-5111 ◽  
Author(s):  
Ren Kong ◽  
Guangbo Yang ◽  
Rui Xue ◽  
Ming Liu ◽  
Feng Wang ◽  
...  
Keyword(s):  
Life Cycle ◽  
Drug Discovery ◽  
Small Molecules ◽  
Web Server ◽  
Supplementary Information ◽  
Binding Modes ◽  
Supplementary Data ◽  
Virus Life Cycle ◽  
Ligand Interactions ◽  
New Type

Abstract Motivation The coronavirus disease 2019 (COVID-19) caused by a new type of coronavirus has been emerging from China and led to thousands of death globally since December 2019. Despite many groups have engaged in studying the newly emerged virus and searching for the treatment of COVID-19, the understanding of the COVID-19 target–ligand interactions represents a key challenge. Herein, we introduce COVID-19 Docking Server, a web server that predicts the binding modes between COVID-19 targets and the ligands including small molecules, peptides and antibodies. Results Structures of proteins involved in the virus life cycle were collected or constructed based on the homologs of coronavirus, and prepared ready for docking. The meta-platform provides a free and interactive tool for the prediction of COVID-19 target–ligand interactions and following drug discovery for COVID-19. Availability and implementation http://ncov.schanglab.org.cn. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles

2021 ◽  
Author(s):  
Davide Risso ◽  
Stefano Maria Pagnotta
Keyword(s):  
Single Cell ◽  
Expression Profiles ◽  
Unsupervised Clustering ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Rna Seq ◽  
Data Transformations ◽  
The Impact

Abstract Motivation Data transformations are an important step in the analysis of RNA-seq data. Nonetheless, the impact of transformation on the outcome of unsupervised clustering procedures is still unclear. Results Here, we present an Asymmetric Winsorization per Sample Transformation (AWST), which is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering. Our procedure leads to robust and biologically meaningful clusters both in bulk and in single-cell applications. Availability The AWST method is available at https://github.com/drisso/awst. The code to reproduce the analyses is available at https://github.com/drisso/awst\_analysis. Supplementary information Supplementary data are available at Bioinformatics online.

HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures

2020 ◽  
Vol 36 (12) ◽  
pp. 3944-3946 ◽  
Author(s):  
Shanyu Chen ◽  
Xiaoyu He ◽  
Ruilin Li ◽  
Xiaohong Duan ◽  
Beifang Niu
Keyword(s):  
Mutation Analysis ◽  
Web Server ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Supplementary Information ◽  
Supplementary Data ◽  
3D Structures ◽  
One Stop ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Abstract Motivation HotSpot3D is a widely used software for identifying mutation hotspots on the 3D structures of proteins. To further assist users, we developed a new HotSpot3D web server to make this software more versatile, convenient and interactive. Results The HotSpot3D web server performs data pre-processing, clustering, visualization and log-viewing on one stop. Users can interactively explore each cluster and easily re-visualize the mutational clusters within browsers. We also provide a database that allows users to search and visualize proximal mutations from 33 cancers in the Cancer Genome Atlas. Availability and implementation http://niulab.scgrid.cn/HotSpot3D/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SEABED: Small molEcule activity scanner weB servicE baseD

2014 ◽  
Vol 31 (5) ◽  
pp. 773-775 ◽  
Author(s):  
Carlos Fenollosa ◽  
Marcel Otón ◽  
Pau Andrio ◽  
Jorge Cortés ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Web Service ◽  
Web Server ◽  
Software As A Service ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Ensemble Docking ◽  
Web Tools ◽  
Protein Mutants ◽  
User Friendly ◽  
Hybrid Docking

Abstract Motivation: The SEABED web server integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. SEABED is not a monolithic workflow tool but Software as a Service platform. Availability and implementation: SEABED is a free web server available athttp://www.bsc.es/SEABED. No registration is required. Contact: [email protected] Supplementary information: Supplementary data are available atBioinformatics online.

scholarly journals Estimating the power of sequence covariation for detecting conserved RNA structure

2020 ◽  
Vol 36 (10) ◽  
pp. 3072-3076 ◽  
Author(s):  
Elena Rivas ◽  
Jody Clements ◽  
Sean R Eddy
Keyword(s):  
Secondary Structure ◽  
Sequence Alignment ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Source Code ◽  
Web Server ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Detection Power ◽  
Non Coding Rnas

Abstract Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures. Availability and implementation The R-scape web server is at eddylab.org/R-scape, with a link to download the source code. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The TMCrys server for supporting crystallization of transmembrane proteins

2019 ◽  
Vol 35 (20) ◽  
pp. 4203-4204
Author(s):  
Julia K Varga ◽  
Gábor E Tusnády
Keyword(s):  
Membrane Proteins ◽  
Structure Determination ◽  
Web Server ◽  
Transmembrane Proteins ◽  
Prediction Method ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Successful Completion ◽  
Determination Process

Abstract Motivation Due to their special properties, the structures of transmembrane proteins are extremely hard to determine. Several methods exist to predict the propensity of successful completion of the structure determination process. However, available predictors incorporate data of any kind of proteins, hence they can hardly differentiate between crystallizable and non-crystallizable membrane proteins. Results We implemented a web server to simplify running TMCrys prediction method that was developed specifically to separate crystallizable and non-crystallizable membrane proteins. Availability and implementation http://tmcrys.enzim.ttk.mta.hu Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals IGLOSS: iterative gapless local similarity search

2019 ◽  
Vol 35 (18) ◽  
pp. 3491-3492
Author(s):  
Braslav Rabar ◽  
Maja Zagorščak ◽  
Strahil Ristov ◽  
Martin Rosenzweig ◽  
Pavle Goldstein
Keyword(s):  
Parameter Estimation ◽  
Similarity Search ◽  
Sequence Similarity ◽  
Web Server ◽  
Supplementary Information ◽  
Local Similarity ◽  
Supplementary Data ◽  
Matching Algorithm ◽  
Local Sequence ◽  
Sequence Patterns

Abstract Summary Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available sequences calls for novel methods to explore local sequence similarity. We have developed a new method for iterative motif scanning that will look for ungapped sequence patterns similar to a submitted query. Using careful parameter estimation and an adaptation of a fast string-matching algorithm, the method performs significantly better in this context than the existing software. Availability and implementation The IGLOSS web server is available at http://compbioserv.math.hr/igloss/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MMseqs2 desktop and local web server app for fast, interactive sequence searches

2019 ◽  
Vol 35 (16) ◽  
pp. 2856-2858 ◽  
Author(s):  
Milot Mirdita ◽  
Martin Steinegger ◽  
Johannes Söding
Keyword(s):  
Protein Sequence ◽  
Response Times ◽  
Web Server ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Server Application ◽  
The Web

Abstract Summary The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST. Availability and implementation The app is easy to install for non-experts. GPLv3-licensed code, pre-built desktop app packages for Windows, MacOS and Linux, Docker images for the web server application and a demo web server are available at https://search.mmseqs.com. Supplementary information Supplementary data are available at Bioinformatics online.

G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram

2019 ◽  
Author(s):  
Xin Guo ◽  
Bo Zhang ◽  
Wenqi Zeng ◽  
Shuting Zhao ◽  
Dongliang Ge
Keyword(s):  
Cancer Genomics ◽  
R Package ◽  
Genetic Mutation ◽  
Supplementary Information ◽  
Genetic Mutations ◽  
Supplementary Data ◽  
High Quality ◽  
Web Browser ◽  
Mutation Data ◽  
Different Levels

Abstract Summary The lollipop-diagram is one of the widely used graphical representations to visualize and explore translational effects of genetic mutations in cancer genomics. However, an easy-to-use lollipop-diagram tool with full functionality is still lacking. Here, we introduce g3viz, an R package that enables researchers to explore genetic mutation data using a lollipop-diagram in a web browser. With a few lines of R code, users can interactively visualize data details, annotate findings and export resultant diagrams in high-quality figures. Because of usefulness and usability, g3viz can be generally exploited by researchers with different levels of bioinformatics skills and programming experience. Availability and implementation The R package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/g3viz). The g3lollipop JavaScript package is freely available under MIT license at GitHub (https://github.com/g3viz/g3lollipop.js). Supplementary information Supplementary data are available at Bioinformatics online.

MODERN PROBLEMS OF ACCOUNTING AND ANALYTICAL ENSURING FINANCIAL RESULTS MANAGEMENT

2020 ◽  
Author(s):  
Yuliia Peniak ◽  
◽  
Nataliia Horokhovatska ◽  
Keyword(s):  
Performance Management ◽  
Enterprise Management ◽  
Goods And Services ◽  
Financial Condition ◽  
General Evaluation ◽  
Net Profit ◽  
Business Entities ◽  
Results Management ◽  
Main Components ◽  
The Impact

The main purpose of any enterprise in the market economy is to obtain high financial results. One of the main conditions for the effective functioning of the enterprise is ability to generate profit in the amount that will create the financial basis for further development and expansion of the enterprise, comply with social and material needs, ensure competitiveness in the market of goods and services. The need for accounting and analytical management of financial results stems from needs of owners, the state and employees in information that will enable them to identify patterns and trends in financial results, identify and assess the main factors influencing the process of their creation, distribution and usage, identify reserves and thus increase the level of profitability. Despite the significant scientific contribution in the field of research of financial results of the enterprises, the issue of improvement aims to the accounting and analytical maintenance of management of financial results of the enterprise remains actual. That is why the purpose of the study is to substantiate the theoretical and practical aspects and develop approaches to improving the mechanism of formation of accounting and analytical support for the management of financial results of the enterprise. Accounting and analytical management of financial results of the enterprise is a set of interconnected elements of production and management system, activities carried out by the subject of management, creation of a certain structure, as well as collection, accumulation, storage and analysis of information necessary for effective operation of the enterprise. The main components of the study of accounting and analytical support of financial performance management are the formation of methods of analysis, control and forecasting of financial results, which requires specification of the components of the analytical and controlled process within the organizational and information model. Namely, the formation of reliable information about the financial condition of the enterprise, the analysis of economic indicators of the enterprise is of great importance in the system of general evaluation of business entities. Their research makes it possible to assess the dynamics of the structure of income and expenses, to determine the impact of factors on the company's profit from various activities, as well as to find reserves to increase the net profit of enterprises. Thus, the improvement of accounting and analytical support of enterprise management is based on the use of modern forms, methods and principles that place new demands on the formation of unbiased, complete, timely, clear and useful accounting and analytical information about the enterprise and its financial results.

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