Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2, 97080 Würzburg Germany.
Gigascience. 2018 Sep 1;7(9):giy096. doi: 10.1093/gigascience/giy096.
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
为了理解感兴趣的生物体的基因调控，全面的基因组注释是必不可少的。虽然有些特征，如编码序列，可以根据基因组序列进行高度准确的计算预测，但其他特征，如启动子元件或非编码 RNA，则更难检测。RNA 测序（RNA-seq）已被证明是一种有效的方法，可以识别这些基因组特征并改进基因组注释。然而，为了生成高分辨率的注释，处理和整合 RNA-seq 数据是具有挑战性的、耗时的，并且需要许多步骤。我们构建了一个名为 ANNOgesic 的强大且模块化的工具，它提供了所需的分析，并简化了基于 RNA-seq 的细菌和古菌基因组注释。它可以整合来自常规 RNA-seq 和差异 RNA-seq 的数据，并以高精度预测和注释许多特征，包括小非编码 RNA。该软件可在开放源代码许可证（ISCL）下在 https://pypi.org/project/ANNOgesic/ 获得。
