Table 9.

Queries used in command-line eutils to collect input datasets for ribodbmaker

Gene	Eutils Query
Archaeal and bacterial SSU rRNA	PRJNA33175[BioProject] OR PRJNA33317[BioProject]
Bacterial LSU rRNA	Bacteria [orgn] AND (23S [ti] OR large subunit ribosomal RNA [ti])
	NOT uncultured [orgn] NOT 23S rRNA methyltransferase [ti] NOT srcdb pdb [prop]
	NOT srcdb PAT [prop] NOT WGS [filter] NOT mRNA [filter] [ti]
	NOT RefSeq [filter] NOT mRNA NOT “mitochondrion”[Filter] NOT TLS [ti]
Archaeal LSU rRNA	Archaea[orgn] AND (23S [ti] OR large subunit ribosomal RNA [ti])
	NOT uncultured [orgn] NOT 23S rRNA methyltransferase[ti] NOT srcdb pdb [prop]
	NOT srcdb PAT [prop] NOT WGS [filter] NOT mRNA [filter] [ti]
	NOT RefSeq [filter] NOT mRNA NOT “mitochondrion”[Filter] NOT TLS [ti]
Eukaryotic SSU rRNA	eukaryota[orgn] (18S [ti] OR small subunit ribosomal RNA [ti])
	NOT WGS [filter] NOT mRNA [filter] NOT “mitochondrion”SSU rRNA [Filter]
	NOT plastid [filter] NOT chloroplast [filter] NOT plastid [ti]
	NOT chloroplast [ti] NOT mitochondrial [ti] NOT RefSeq [filter]
	NOT (5.8S [ti] OR internal [ti]) NOT 28S [ti] NOT WGS NOT mRNA
	NOT “mitochondrion”[Filter] NOT TLS [ti] NOT srcdb pdb[prop]
Eukaryotic LSU rRNA	Eukaryota[orgn] AND (25S [ti] OR 26S [ti] OR 28S [ti] OR large subunit
	Ribosomal RNA [ti]) NOT WGS [filter] NOT mRNA [filter] NOT “mitochondrion”
	[Filter] NOT plastid [filter] NOT chloroplast [filter] NOT plastid [ti]
	NOT chloroplast [ti] NOT mitochondrial [ti] NOT RefSeq [filter] NOT
	(5.8S [ti] OR internal [ti]) NOT TLS [ti] NOT partial cds [ti] NOT
	Chain [ti] NOT 18S [ti] NOT srcdb pdb [prop]
Microsporidia SSU rRNA	Microsporidia [orgn] AND (18S [ti] OR small subunit ribosomal RNA [ti])
	NOT WGS [filter] NOT mRNA [filter] NOT “mitochondrion”[Filter]
	NOT plastid [filter] NOT chloroplast [filter] NOT plastid [ti]
	NOT chloroplast [ti] NOT mitochondrial [ti] NOT RefSeq [filter]
	NOT (5.8S [ti] OR internal [ti]) NOT 28S [ti] NOT WGS NOT mRNA
	NOT “mitochondrion”[Filter] NOT TLS [ti] NOT srcdb pdb[prop]
Microsporidia LSU rRNA	Microsporidia [orgn] AND (25S [ti] OR 26S [ti] OR 28S [ti] OR large subunit
	Ribosomal RNA [ti]) NOT WGS [filter] NOT mRNA [filter] NOT “mitochondrion”
	[Filter] NOT plastid [filter] NOT chloroplast [filter] NOT plastid [ti]
	NOT chloroplast [ti] NOT mitochondrial [ti] NOT RefSeq [filter]
	NOT (5.8S [ti] OR internal [ti]) NOT TLS [ti] NOT partial cds [ti]
	NOT Chain [ti] NOT 18S [ti] NOT srcdb pdb [prop]
Fungal SSU rRNA RefSeq records	Fungi [orgn] AND 225:10000 [slen] AND sequence from type [filter]
	AND (18S [ti] OR small subunit ribosomal RNA [ti]) NOT WGS [filter]
	NOT mRNA [filter] NOT mitochondrion [Filter] NOT plastid [filter]
	NOT chloroplast [filter] NOT mitochondrial [ti] NOT (5.8S [ti] OR internal [ti])
	NOT 28S [ti] NOT 26S [ti] NOT 25S [ti] NOT 5S [ti] NOT 23S [ti] NOT 37S [ti]
	NOT WGS NOT mRNA NOT RefSeq [filter] NOT TLS [ti]
Fungal LSU rRNA RefSeq records	Fungi [orgn] AND 425:10000[slen] AND sequence from type[filter]
	AND (25S[ti] OR 26S[ti] OR 28S [ti] OR large subunit ribosomal RNA[ti])
	NOT WGS[filter] NOT mRNA [filter] NOT “mitochondrion”[Filter]
	NOT plastid [filter] NOT chloroplast [filter] NOT mitochondrial [ti]
	NOT (5.8S [ti] OR internal [ti]) NOT TLS [ti] NOT partial cds [ti]
	NOT Chain [ti] NOT 18S [ti] NOT srcdb pdb [prop] NOT RefSeq [filter]