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. Palindrome analyser also features an interactive graphical data representation of the distribution of the inverted repeats, with options for sorting according to the length of inverted repeat, length of loop, and number of mismatches. Palindrome analyser can be accessed at http://bioinformatics.ibp.cz.

Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 612 65 Brno Czech Republic

Mendel University in Brno Zemědělská 1 613 00 Brno Czech Republic

References provided by Crossref.org

CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome

Special Issue "Bioinformatics of Unusual DNA and RNA Structures"

Variability of Inverted Repeats in All Available Genomes of Bacteria

Genomic Analysis of Non-B Nucleic Acids Structures in SARS-CoV-2: Potential Key Roles for These Structures in Mutability, Translation, and Replication?

Inverted repeats in the monkeypox virus genome are hot spots for mutation

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

A new lineage of non-photosynthetic green algae with extreme organellar genomes

R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains

Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences

SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci

G-Quadruplexes in the Archaea Domain

In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles

The Rich World of p53 DNA Binding Targets: The Role of DNA Structure

G4Hunter web application: a web server for G-quadruplex prediction

The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

p73, like its p53 homolog, shows preference for inverted repeats forming cruciforms

Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability