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.
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