Publication result detail

Feature-overlapper: The tool for DNA analysis overlap

HAVLÍK, J.; BRÁZDA, V.; STANĚK, K.; JEŽEK, M.; ŠŤASTNÝ, J.

Original Title

Feature-overlapper: The tool for DNA analysis overlap

English Title

Feature-overlapper: The tool for DNA analysis overlap

Type

WoS Article

Original Abstract

This contribution puts focus on a command line tool, which enables detection and analysis of overlapping regions between G-quadruplexes, R-loops and genome annotations for selected genomes. G-quadruplexes and R-loops are structures with high Guanine density, which is an important creation factor for both structures. Common regions (overlap) between both structures can provide us with better possibility to create precise model to detect R-loops and valuable insights when inspecting genome annotations with high R-loop density. The tool was used for multiple research projects and is under constant development bringing new features to the world of bioinformatics.

English abstract

This contribution puts focus on a command line tool, which enables detection and analysis of overlapping regions between G-quadruplexes, R-loops and genome annotations for selected genomes. G-quadruplexes and R-loops are structures with high Guanine density, which is an important creation factor for both structures. Common regions (overlap) between both structures can provide us with better possibility to create precise model to detect R-loops and valuable insights when inspecting genome annotations with high R-loop density. The tool was used for multiple research projects and is under constant development bringing new features to the world of bioinformatics.

Keywords

DNA; R-loop; G-quadruplex; Annotation

Key words in English

DNA; R-loop; G-quadruplex; Annotation

Authors

HAVLÍK, J.; BRÁZDA, V.; STANĚK, K.; JEŽEK, M.; ŠŤASTNÝ, J.

RIV year

2024

Released

01.05.2023

Publisher

Elsevier

Location

AMSTERDAM

ISBN

2665-9638

Periodical

Software Impacts

Volume

16

Number

5

State

Kingdom of the Netherlands

Pages from

1

Pages to

4

Pages count

4

URL

https://www.sciencedirect.com/science/article/pii/S2665963823000350?via%3Dihub

Full text in the Digital Library

http://hdl.handle.net/11012/213660

BibTex

@article{BUT183463,
  author="Jan {Havlík} and Václav {Brázda} and Kamil {Staněk} and Michal {Ježek} and Jiří {Šťastný}",
  title="Feature-overlapper: The tool for DNA analysis overlap",
  journal="Software Impacts",
  year="2023",
  volume="16",
  number="5",
  pages="1--4",
  doi="10.1016/j.simpa.2023.100498",
  issn="2665-9638",
  url="https://www.sciencedirect.com/science/article/pii/S2665963823000350?via%3Dihub"
}

Documents

1-s2.0-S2665963823000350-main