Publication detail

Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

BRÁZDA, V. KOLOMAZNÍK, J. LÝSEK, J. HÁRONÍKOVÁ, L. COUFAL, J. ŠŤASTNÝ, J.

Original Title

Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

Type

journal article in Web of Science

Language

English

Original Abstract

DNA cruciform structures play an important role in the regulation of natural processes including gene replication and expression, as well as nucleosome structure and recombination. They have also been implicated in the evolution and development of diseases such as cancer and neurodegenerative disorders. Cruciform structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling and protein binding. They have received broad attention because of their important roles in biology. Computational approaches to study inverted repeats have allowed detailed analysis of genomes. However, currently there are no easily accessible and user-friendly tools that can analyse inverted repeats, especially among long nucleotide sequences. We have developed a web-based server, Palindrome analyser, which is a user-friendly application for analysing inverted repeats in various DNA (or RNA) sequences including genome sequences and oligonucleotides. It allows users to search and retrieve desired gene/nucleotide sequence entries from the NCBI databases, and provides data on length, sequence, locations and energy required for cruciform formation.

Keywords

Palindrome analyser, web-based server, inverted repeats, nucleotide sequences, DNA sequences

Authors

BRÁZDA, V.; KOLOMAZNÍK, J.; LÝSEK, J.; HÁRONÍKOVÁ, L.; COUFAL, J.; ŠŤASTNÝ, J.

Released

30. 9. 2016

ISBN

0006-291X

Periodical

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Year of study

479

Number

2

State

United States of America

Pages from

1739

Pages to

1745

Pages count

7

URL

http://www.sciencedirect.com/science/article/pii/S0006291X16314620

BibTex

@article{BUT128435,
  author="Václav {Brázda} and Jan {Kolomazník} and Jiří {Lýsek} and Jan {Coufal} and Jiří {Šťastný}",
  title="Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences",
  journal="BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS",
  year="2016",
  volume="479",
  number="2",
  pages="1739--1745",
  doi="10.1016/j.bbrc.2016.09.015",
  issn="0006-291X",
  url="http://www.sciencedirect.com/science/article/pii/S0006291X16314620"
}