ArticleGigaScience2018
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed.
- Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host-microbe communication.Archives of microbiology · 2026Review
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene.RNA biology · 2025Article
- Regulation of the tagatose catabolic gene cluster and development of a tagatose-inducible expression system in the probiotic Escherichia coli Nissle 1917.Microbial cell factories · 2025Article
- High quality transcriptome profiling confirms the transcriptional landscape of Treponema pallidum subsp. pallidum.Scientific reports · 2025Article
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- TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.NAR genomics and bioinformatics · 2024Article
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Transcriptome fine-mapping inmBio · 2024Article
- An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity.Nature microbiology · 2024Article
- Article
- Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency inPNAS nexus · 2023Article
- CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.Journal of industrial microbiology & biotechnology · 2023Article
- High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5International journal of molecular sciences · 2022Article
- Posttranscriptional Regulation in Response to Different Environmental Stresses in Campylobacter jejuni.Microbiology spectrum · 2022Article
- Small open reading frames in plant research: from prediction to functional characterization.3 Biotech · 2022Review
- Small Proteins in Archaea, a Mainly Unexplored World.Journal of bacteriology · 2022Review
- CRISPR genome editing using computational approaches: A survey.Frontiers in bioinformatics · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.