The BSGatlas: An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access [article]

Adrian Sven Geissler, Christian Anthon, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Stefan Ernst Seemann, Jeppe Vinther, Jan Gorodkin
2019 bioRxiv   pre-print
The genome of Bacillus subtilis continues to provide exiting genomic insights. However, the growing collective genomic knowledge about this micro-organism is spread across multiple annotation resources. Thus, the full annotation is not directly accessible neither for specific genes nor for large-scale high-throughput analyses. Furthermore, access to annotation of non-coding RNA genes (ncRNAs) and polycistronic mRNAs is difficult. To address these challenges we introduce the Bacillus subtilis
more » ... ome atlas, BSGatlas, in which we integrate and unify multiple existing annotation resources. Our integration provides twice as many ncRNAs than the individual resources, improves the positional annotation for 70% of the combined ncRNAs, and makes it possible to infer specific ncRNA types. Moreover, we unify known transcription start sites, termination, and transcriptional units (TUs) as a comprehensive transcript map. This transcript map implies 815 new TUs and 6,164 untranslated regions (UTRs), which is a five-fold increase over existing resources. We furthermore, find 2,309 operons covering the transcriptional annotation for 93% of all genes, corresponding to an improvement by 11%. The BSGatlas is available in multiple formats. A user can either download the entire annotation in the standardized GFF3 format, which is compatible with most bioinformatics tools for omics and high-throughput studies, or view the annotation in an online browser at http://rth.dk/resources/bsgatlas.
doi:10.1101/807263 fatcat:5fxkvbgbofg23dscplqwxgjnda