Table 1.

An overview of relevant B. subtilis annotation resources.

The first column provides the resource name. Resources marked with * were considered for integration into the BSGatlas. The remaining resources were already fully contained in at least one of the utilized resources. (Based on a trivial coordinate comparison, not shown). The second column gives a short description and the third the kind of annotations it provides.

Resource	General description	Provided annotation
RefSeq* [24]	Large collection of reference sequences including annotations Contains B. subtilis 168 standard annotation Most commonly used B. subtilis annotation resource	Coding genes All rRNAs, tRNAs of B. subtilis Only few other ncRNAs No mRNA transcripts
DBTBS* [27]	Collection of transcriptional binding factors Literature curated database	Operons TSSs/TTSs
BsubCyc* [35]	B. subtilis specific database Encyclopaedia of metabolism and pathways	Coding genes All rRNAs, tRNAs Only few other ncRNAs Few transcripts with TSSs and TTSs
SubtiWiki* [8]	B. subtilis specific database Active community annotation effort Functional annotation driven Does not provide coordinates	Coding genes All rRNAs, tRNAs Many additional ncRNAs TUs
Nicolas et al.* [4]	Tilling-array study in B. subtilis Transcriptome in over >100 conditions Large number of predictions Technical resolution limitation	Many predicted ncRNAs Many predicted TSSs/TTSs Explicitly annotates UTRs
Dar et al.* [26]	Term-seq study in B. subtilis	Riboswitches
Rfam* [38]	Database of RNA structure families We scanned B. subtilis genome with most recent Rfam version Database of RNA structure families	All rRNAs, tRNAs Riboswitches sRNAs and other structured RNAs
Ensembl [85]	B. subtilis specific database Active community annotation effort Functional annotation driven Does not provide coordinates	Coding genes All rRNAs, tRNAs Only few other ncRNAs No mRNA transcripts
PARTIC [29]	Integrative database of bacterial genomes Analysis tools to support biomedical research Uses different genome sequence than RefSeq But nearly identical on annotated gene set	Coding genes All rRNAs, tRNAs Only few other ncRNAs No mRNA transcripts
IMG/M [30]	Integrative database of Archaea, Bacteria and Eukarya Tools for comparative genome analysis Uses RefSeq as reference	Coding genes All rRNAs, tRNAs Only few other ncRNAs No mRNA transcripts
BSRD [33]	Single ncRNA type specific database Already included in other resources	sRNA
SRPDB [31]	Single ncRNA type specific database Already included in other resources	SRP
tmRDB [31]	Single ncRNA type specific database Already included in other resources	tmRNA
tmRNA [34]	Single ncRNA type specific database Already included in other resources	tmRNA
tRNAdb [32]	Single ncRNA type specific database Already included in other resources	tRNA