YcaO Biosynthetic Gene Clusters in Actinobacteria

1,464 GenBank files retrieved and annotated by RiPPER (https://github.com/streptomyces/ripper; RiPPER originally reported in https://academic.oup.com/nar/article/47/9/4624/5420534) using standalone YcaO proteins from Actinobacteria as the input. This dataset also includes 6 entries from Firmicutes that are reported in the associated manuscript (see reference below). The GenBank files represent putative biosynthetic gene clusters associated with YcaO domain proteins. <br><br>The files are named with the species name and the accession of the input YcaO protein. <br><br>When viewed in the Artemis genome browser (Wellcome Sanger Institute), the input YcaO protein is coloured green and short peptides (&lt;120 amino acids) annotated by RiPPER are colour-coded based on their relative Prodigal score, which indicates the likelihood of being true protein-coding genes. This is a scale from pale red (low score) to magenta (high score). Associated peptide data is deposited with the manuscript.<br>

本数据集包含1,464个GenBank文件（GenBank files），由RiPPER工具（https://github.com/streptomyces/ripper；RiPPER最初发表于论文：https://academic.oup.com/nar/article/47/9/4624/5420534）检索并注释，以来自放线菌门（Actinobacteria）的独立YcaO蛋白（YcaO protein）作为输入数据集。此外，本数据集还纳入了随附手稿中报道的6条来自厚壁菌门（Firmicutes）的条目（详见下文参考文献）。这些GenBank文件对应与YcaO结构域蛋白相关的推定生物合成基因簇。<br><br>数据集文件以物种名加上输入YcaO蛋白的登录号进行命名。<br><br>在Artemis基因组浏览器（Artemis genome browser，惠康桑格研究所Wellcome Sanger Institute）中查看时，输入的YcaO蛋白将以绿色标注；由RiPPER注释的短肽（氨基酸残基数<120）则根据其相对Prodigal评分（Prodigal score）进行颜色编码，该评分可反映其作为真实蛋白编码基因的可能性，颜色梯度从浅红色（低分）至品红色（高分）。相关肽段数据已随手稿一并提交存档。