Highlights•RNA-seq has become the method of choice for bacterial transcriptomics.•
Differential RNA-seq (dRNA-seq) distinguishes primary and processed transcripts.•dRNA …

While the model organism Escherichia coli has been the subject of intense study for
decades, the full complement of its RNAs is only now being examined. Here we describe a …

CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset
to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the …

NAD is a coenzyme central to metabolism that also serves as a 5′-terminal cap for bacterial
and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and …

Recent advances in long-read sequencing solve inaccuracies in alternative transcript
identification of full-length transcripts in short-read RNA-Seq data, which encourages the …

The human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The
complete viral genome is transcriptionally active during infection; however, a large part of its …

Motivation: The vast amount of already available and currently generated read mapping
data requires comprehensive visualization, and should benefit from bioinformatics tools …

The emerging human enteropathogen Clostridioides difficile is the main cause of diarrhea
associated with antibiotherapy. Regulatory pathways underlying the adaptive responses …

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 …

The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen
baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the …