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.

English 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

en

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.

English 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 in English

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

Released

30.09.2016

ISSN

0006-291X

Volume

479

Number

2

Pages from–to

1739–1745

Pages count

7

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",
  year="2016",
  volume="479",
  number="2",
  month="September",
  pages="1739--1745",
  issn="0006-291X"
}