Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences.
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. Electronic address: vaclav@ibp.cz.
Václav
V
Brázda
Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
Jan
J
Kolomazník
Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
Jiří
J
Lýsek
Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
Lucia
L
Hároníková
Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
Jan
J
Coufal
Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
Jiří
J
Št'astný
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000032:analysis / Q000235:genetics*; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D045566:DNA, Cruciform / Q000032:analysis / Q000235:genetics; D004279:DNA, Viral / Q000032:analysis / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D020407:Internet; D055029:Inverted Repeat Sequences / Q000235:genetics*; D009841:Oligonucleotides / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D014780:Viruses / Q000145:classification / Q000235:genetics
D004269:DNA, Bacterial; D045566:DNA, Cruciform; D004279:DNA, Viral; D009841:Oligonucleotides; D004247:DNA