DNA Punctuation: Genome Annotations with Stem-Loop Structures

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.

本团队研发了一套计算机程序，名为DNA标点（www.dnapunctuation.org），该程序可在用户定义的茎环结构大小范围和错配数范围内搜索并报告所有可能的茎环结构。借助DNA标点，我们对2030种细菌和古菌的全基因组以及人类基因组进行了短和长茎环结构的注释。我们提供了三种版本的基因组注释：包含茎环和所有可能变体的完整注释、不含变体的注释，以及基因组序列完整版本，其中被茎环覆盖的区域以小写字母形式表示。网站www.dnapunctuation.org提供了该程序的命令行和图形界面版本，用户可通过定义参数进行全基因组或基因组片段的注释。