R (software) Dotaz Zobrazit nápovědu

R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA-DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.

MeSH
algoritmy * MeSH
DNA chemie genetika MeSH
genomika metody MeSH
internet statistika a číselné údaje MeSH
lidé MeSH
nestabilita genomu * MeSH
R-smyčka * MeSH
software MeSH
Check Tag
lidé MeSH
Publikační typ
časopisecké články MeSH

Abstrakt

Systém R jako nástroj statistické analýzy v biomedicínském výzkumu [R system as a statistical analysis instrument in biomedical research]

Besides traditional program systems such as SPSS or STATISTICA, rising popularity of R system with its ...

, že vedle tradičních programových systému jako SPSS nebo STATISTICA se stále více prosazuje systém R ...

Hendl, Jan, 1947-
Autor Autorita Fakulta tělesné výchovy a sportu Univerzity Karlovy, katedra základů kinatropologie

Medsoft .... 2012 ; () : 104-121.

ISSN 1803-8115
Medvik
Zdroj

Příspěvek pojednává některé aspekty využívání programů pro statistickou analýzu. Ukazuje se, že vedle tradičních programových systému jako SPSS nebo STATISTICA se stále více prosazuje systém R se svým programovacím jazykem. Tento systém má dvě hlavní výhody. Je volně šiřitelný stejně jako programové balíčky, které jsou v něm vytvářeny. Existuje již několik tisíc programových balíčku v jazyce R pro nejrůznější úkoly statistické analýzy. Pojednáváme základy systému R a některé rozšiřující programové balíčky.

The paper discusses some aspects of using statistical analysis programs. Besides traditional program systems such as SPSS or STATISTICA, rising popularity of R system with its own programming language has been seen. This system entails two principal advantages. It can be freely distributed, similarly as its program packages created in its environment. Currently, several thousand program packages in the R language exist for varied tasks of statistical analysis. This paper discusses the basics of the R system, as well as some extension program packages.

Klíčová slova
systém R,
MeSH
automatizované zpracování dat metody MeSH
biomedicínský výzkum metody MeSH
programovací jazyk MeSH
software MeSH
statistika jako téma MeSH

Článek

Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software

different experimental and/or instrumental setups usually require the use of multiple data analysis software ...

Journal of proteome research. 2021 ; 20 (1) : 776-785. [pub] 20200928

J Proteome Res
ISSN 1535-3907
Medvik
Zdroj

Identification of metal-binding sites in proteins and understanding metal-coupled protein folding mechanisms are aspects of high importance for the structure-to-function relationship. Mass spectrometry (MS) has brought a powerful adjunct perspective to structural biology, obtaining from metal-to-protein stoichiometry to quaternary structure information. Currently, the different experimental and/or instrumental setups usually require the use of multiple data analysis software, and in some cases, they lack some of the main data analysis steps (MS processing, scoring, identification). Here, we present a comprehensive data analysis pipeline that addresses charge-state deconvolution, statistical scoring, and mass assignment for native MS, bottom-up, and native top-down with emphasis on metal-protein complexes. We have evaluated all of the approaches using assemblies of increasing complexity, including free and chemically labeled proteins, from low- to high-resolution MS. In all cases, the results have been compared with common software and proved how MetaOdysseus outperformed them.