title: Species-specific typing of DNA based on palindrome frequency patterns.
abstract: DNA in its natural, double-stranded form may contain palindromes, sequences which read the same from either side because they are identical to their reverse complement on the sister strand. Short palindromes are underrepresented in all kinds of genomes. The frequency distribution of short palindromes exhibits more than twice the inter-species variance of non-palindromic sequences, which renders palindromes optimally suited for the typing of DNA. Here, we show that based on palindrome frequency, DNA sequences can be discriminated to the level of species of origin. By plotting the ratios of actual occurrence to expectancy, we generate palindrome frequency patterns that allow to cluster different sequences of the same genome and to assign plasmids, and in some cases even viruses to their respective host genomes. This finding will be of use in the growing field of metagenomics.
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
authors.forename: Estelle
authors.initials: E
authors.lastname: Lamprea-Burgunder
authors.forename: Philipp
authors.initials: P
authors.lastname: Ludin
authors.forename: Pascal
authors.initials: P
authors.lastname: Mäser
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D016000:Cluster Analysis; D004247:DNA / Q000145:classification* / Q000235:genetics*; D016172:DNA Fingerprinting; D014644:Genetic Variation; D016678:Genome / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics*; D056186:Metagenomics; D013045:Species Specificity; D015003:Yeasts / Q000235:genetics
chemical_list: D004247:DNA