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Table 9 Queries used in command-line eutils to collect input datasets for ribodbmaker

From: Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

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]