Genome annotation with short stem-loop structures

These examples made it possible for a librarian of genius to discover
the fundamental law of the Library. This thinker observed that all the books, no
matter how diverse they might be, are made up of the same elements: the space,
the period, the comma, the twenty-two letters of the alphabet.

Jorge Luis Borges "The Library of Babel"
Project Information
Since the famous discovery of DNA structure by Watson and Crick as a double-helix, which is known as canonical right-handed B form, or B-DNA conformation, they have been experimental evidences about existence of so-called non-B DNA conformations. These non-B DNA structures include A-DNA, Z-DNA, triplexes, stem-loops (also known as cruciforms or hairpins), nodule DNA, G4 tetrad (tetraplexes), and some other non-canonical structures.

Here we focus on one class of non-B DNA structures called stem-loops, also referred as hairpins and cruciforms. Stem-loop structures are formed from short palindromic DNA sequences with a spacer. If structure is formed in a single-stranded DNA it is called a hairpin. In double stranded DNA two hairpins could protrude symmetrically from both strands creating a cruciform. The important role of stem-loops in various genomic processes as terminators, attenuators, promoters and recombination marks has been documented experimentally.

Here we provide an open resource with genomes annotated and masked with short palidnromic structures. Currently it includes more than 2000 bacterial and archaeal genomes, and human genome, version hg19.