ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

GigaScience
Sung-Huan YuKonrad U Förstner

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/.

References

Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Jun 28, 2005·Nucleic Acids Research·Peter SchattnerTodd M Lowe
Feb 1, 2006·Bioinformatics·Ulrike MücksteinIvo L Hofacker
Jul 18, 2006·Nucleic Acids Research·Timothy L BaileyWilfred W Li
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Apr 25, 2008·Bioinformatics·Hakim Tafer, Ivo L Hofacker
Apr 26, 2008·PLoS Computational Biology·Martin C FrithTimothy L Bailey
May 30, 2008·Nucleic Acids Research·Sun KimByoung-Tak Zhang
Oct 18, 2008·Nucleic Acids Research·Kim D PruittDonna R Maglott
Dec 30, 2008·Molecular Cell·Marie BouvierJörg Vogel
Jan 6, 2009·Molecular Microbiology·Matthew R HemmKenneth E Rudd
Feb 26, 2009·Cell·Lauren S Waters, Gisela Storz
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 15, 2009·PLoS Computational Biology·Steve HoffmannJörg Hackermüller
Nov 4, 2009·Genome Research·Omri WurtzelRotem Sorek
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jul 6, 2010·Genome Biology·Elizabeth T CirulliUNKNOWN Center for HIV/AIDS Vaccine Immunology (CHAVI)
Nov 26, 2010·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Feb 11, 2011·Nucleic Acids Research·Thomas D OttoMatthew Berriman
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Oct 2, 2012·Current Opinion in Biotechnology·Kai-Oliver MutzFrank Stahl
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 4, 2012·Nucleic Acids Research·Lei LiHoi Shan Kwan
Jan 18, 2013·RNA Biology·Arthur BeauregardJoseph T Wade
Feb 12, 2013·Bioinformatics·Samuel C ForsterPaul J Hertzog
May 30, 2013·Nucleic Acids Research·Ryan McClureBrian Tjaden
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
Jan 29, 2014·Nature Reviews. Genetics·Nicholas T Ingolia
Mar 4, 2014·Nature Biotechnology·Jeffry D Sander, J Keith Joung
Mar 13, 2014·Annual Review of Biochemistry·Gisela StorzKumaran S Ramamurthi
Mar 20, 2014·Bioinformatics·Torsten Seemann
Mar 29, 2014·BMC Bioinformatics·Fabian AmmanSven Findeiß

❮ Previous
Next ❯

Citations

May 31, 2019·Nucleic Acids Research·Simon LeonardSylvie Reverchon
Feb 28, 2020·Briefings in Bioinformatics·Liang ChenGarry Wong
Dec 17, 2020·Frontiers in Cellular and Infection Microbiology·Charlotte MichauxJörg Vogel
Mar 10, 2020·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Philip P Adams, Gisela Storz
Jul 10, 2021·Nature Microbiology·Falk PonathJörg Vogel
Sep 21, 2021·Journal of Bacteriology·Katrin WeidenbachRuth A Schmitz

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE67564
SRR031126
MG1655
GSE55199
GSE45443

Methods Mentioned

BETA
RNA-seq
dRNA-seq

Software Mentioned

STRING
Python
segemehl
SAMtools
GLAM2
ConsPred
TransTermHP
RNAplex
Prokka
PSORTb

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

Related Papers

Current Opinion in Biotechnology
Aaron J Windsor, Thomas Mitchell-Olds
Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Chengpu ZhangYunping Zhu
© 2022 Meta ULC. All rights reserved