Refine
Has Fulltext
- yes (25)
Is part of the Bibliography
- yes (25)
Year of publication
Document Type
- Journal article (25)
Language
- English (25)
Keywords
- RNA-seq (4)
- escherichia coli (3)
- transcriptomics (3)
- Antisense RNA (2)
- Rhodobacter sphaeroides (2)
- bacteria (2)
- dRNA-Seq (2)
- gene expression (2)
- genome annotation (2)
- identification (2)
- 5-bromodeoxyuridine (1)
- Archaea (1)
- Bacteriaophage AR9 (1)
- Bradyrhizobium (1)
- CRISPR-Cas system (1)
- CRISPRs (1)
- DNA glycosation (1)
- DNA methylation (1)
- DNA methylferase homolog (1)
- Dictyostelium discoideum (1)
- Elektronisches Publizieren (1)
- Erwinia amylovora (1)
- Genome re-annotation (1)
- Haloferax volcanii (1)
- Hfq (1)
- Internal transcription start site (1)
- K279a (1)
- Leaderless transcript (1)
- Methanosarcina mazei (1)
- Neisseria meningitidis (1)
- Nodule (1)
- Non-coding RNAs (1)
- OxyR (1)
- ProQ (1)
- Promoter (1)
- Promoter prediction (1)
- Proteogenomics (1)
- RNA CHAPERONE HFQ (1)
- RNA expression (1)
- RNA sequencing (1)
- RNA sequencing (RNA-Seq) (1)
- RNA-binding proteins (1)
- RNA-polymerase-II (1)
- RNAseq (1)
- RNase E (1)
- RbdB (1)
- SEQ (1)
- SWI2/SNF2-like protein (1)
- Sinorhizobium fredii (1)
- Stenotrophomonas maltophilia (1)
- TRNA(ASP) (1)
- Transcription profiling (1)
- Transcription start site (1)
- Transcriptome (1)
- adaptation phase (1)
- anti-sigma factor (1)
- antibiotic resistance (1)
- antisense RNA (1)
- antisense RNAs (1)
- archaea (1)
- bacillus subtilis (1)
- bacterial genomics (1)
- bacterial pathogen (1)
- beta-lactamases (1)
- binding (1)
- biofilms (1)
- biology (1)
- blood-brain barrier (1)
- blood-cerebrospinal fluid barrier (1)
- brain endothelial cells (1)
- burkholderia cenocepacia (1)
- campylobacter (1)
- casposon (1)
- cepedia complex (1)
- characterization (1)
- colony morphotypes (1)
- dependent gene-expression (1)
- drospophila (1)
- dsRNA binding protein (1)
- emotional behavior (1)
- flagellar basal body (1)
- genome (1)
- genome-wide analysis (1)
- genomic islands (1)
- genomic libraries (1)
- genomic library construction (1)
- genomics (1)
- global gene expression (1)
- gram-negative bacteria (1)
- hela cells (1)
- hydrogen regulation (1)
- hydrogen-peroxide (1)
- hyperthermophile (1)
- in-vivo (1)
- iron limitation (1)
- mass spectrometry (1)
- maternal separation (1)
- mechanism (1)
- membrane vesicles (1)
- meningococcus (1)
- messenger RNA (1)
- messenger-RNA (1)
- metagenomics (1)
- metaproteomics (1)
- metatranscriptomics (1)
- methanoarchaea (1)
- microalga-bacteria interaction (1)
- microbiology (1)
- microprocessor (1)
- mouse (1)
- noncoding RNA (1)
- nosocomial pathogen (1)
- organohalide respiration (1)
- oxidative stress (1)
- pathogen (1)
- persistence (1)
- persister cells (1)
- phenotypic heterogeneity (1)
- photooxidative stress (1)
- photosynthesis genes (1)
- phototrophic growth (1)
- phycosphere biofilm (1)
- plant symbioses (1)
- plasmid copy number (1)
- polycistronic transcription (1)
- posttranscriptional control (1)
- promoters (1)
- protein HFQ (1)
- pseudomas aeruginosa (1)
- quanititative proteomics (1)
- quorum sensing (QS) (1)
- red fluorescent protein (1)
- regulatory small RNAs (1)
- reputation (1)
- resistance (1)
- rhodobacter sphaeroides (1)
- riboswitch (1)
- sRNA (1)
- scholarly publishing (1)
- scientific publishing (1)
- sequence motif analysis (1)
- serotonin (1)
- singlet oxygen stress (1)
- sinorhizobium fredii NGR234 (1)
- small RNAs (1)
- small non-coding RNAs (1)
- stem cells (1)
- streptococcus pneumoniae (1)
- stress resistance (1)
- tetrachloroethene (1)
- transcription start site (1)
- transcriptional regulation (1)
- transcriptome (1)
- transcriptome analysis (1)
- translation initiation (1)
- transport systems (1)
- two‐component system (1)
- variant surface glycoprotein (1)
- version control (1)
- wikis (1)
- xanthomonas maltophilia (1)
Institute
Sonstige beteiligte Institutionen
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/.