ArticleMicrobial genomics2024
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes.Nucleic acids research · 2025Article
- An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis.PLoS genetics · 2025Article
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
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Authors and funding
3 authors.
Funding
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Abstract
Accurate annotation to single-nucleotide resolution of the transcribed regions in genomes is key to optimally analyse RNA-seq data, understand regulatory events and for the design of experiments. However, currently most genome annotations provided by GenBank generally lack information about untranslated regions. Additionally, information regarding genomic locations of non-coding RNAs, such as sRNAs, or anti-sense RNAs is frequently missing. To provide such information, diverse RNA-seq technologies, such as Rend-seq, have been developed and applied to many bacterial species. However, incorporating this vast amount of information into annotation files has been limited and is bioinformatically challenging, resulting in UTRs and other non-coding elements being overlooked or misrepresented. To overcome this problem, we present pyRAP (python Rend-seq Annotation Pipeline), a software package that analyses Rend-seq datasets to accurately resolve transcript boundaries genome-wide. We report the use of pyRAP to find novel transcripts, transcript isoforms, and RNase-dependent sRNA processing events. In
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