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ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
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,...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123526/ https://www.ncbi.nlm.nih.gov/pubmed/30169674 http://dx.doi.org/10.1093/gigascience/giy096 |
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author | Yu, Sung-Huan Vogel, Jörg Förstner, Konrad U |
author_facet | Yu, Sung-Huan Vogel, Jörg Förstner, Konrad U |
author_sort | Yu, Sung-Huan |
collection | PubMed |
description | 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/. |
format | Online Article Text |
id | pubmed-6123526 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-61235262018-09-10 ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes Yu, Sung-Huan Vogel, Jörg Förstner, Konrad U Gigascience Technical Note 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/. Oxford University Press 2018-08-30 /pmc/articles/PMC6123526/ /pubmed/30169674 http://dx.doi.org/10.1093/gigascience/giy096 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Technical Note Yu, Sung-Huan Vogel, Jörg Förstner, Konrad U ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title | ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title_full | ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title_fullStr | ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title_full_unstemmed | ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title_short | ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes |
title_sort | annogesic: a swiss army knife for the rna-seq based annotation of bacterial/archaeal genomes |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123526/ https://www.ncbi.nlm.nih.gov/pubmed/30169674 http://dx.doi.org/10.1093/gigascience/giy096 |
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