Universität zu Köln

Yu, Sung-Huan ORCID: 0000-0001-7955-8645, Vogel, Joerg and Foerstner, Konrad U. (2018). ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. GigaScience, 7 (9). OXFORD: OXFORD UNIV PRESS. ISSN 2047-217X

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Abstract

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/.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Yu, Sung-Huan UNSPECIFIED orcid.org/0000-0001-7955-8645 UNSPECIFIED Vogel, Joerg UNSPECIFIED UNSPECIFIED UNSPECIFIED Foerstner, Konrad U. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-175920
DOI:	10.1093/gigascience/giy096
Journal or Publication Title:	GigaScience
Volume:	7
Number:	9
Date:	2018
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	2047-217X
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language START SITES; TRANSCRIPTOME; PREDICTION; REVEALS; BINDING; DISCOVERY; PROTEINS; TOOL; HFQ; DNA Multiple languages Biology; Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/17592