DNA Punctuation: Genome Annotations with Stem-Loop Structures

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Description: We developed a computer program, DNA Punctuation (www.dnapunctuation.org) that searches and reports all possible stem-loop structures within the user-defined range of stem and loop sizes and the number of mismatches. With DNA Punctuation we annotated full genomes of 2030 bacteria and archaea, and the human genome with short and long stem-loop structures. We provide genome annotations in three versions: complete annotations with stem-loops and all possible variants, annotations without variants, and full genome sequences with regions covered by stem-loops being masked in low case. The web-site www.dnapunctuation.org contains both command line and graphical version of the program, which can be used for the full-genome or genomic fragment annotations with the user-defined parameters.

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