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

BMC Bioinformatics

Table 3 Profile models used by Ribovore

Model name	Gene	Taxonomy group	#Seqs	Length	Rfam
SSU_rRNA_archaea	SSU rRNA	Archaea	86	1477	RF01959
SSU_rRNA_bacteria	SSU rRNA	Bacteria	99	1533	RF00177
SSU_rRNA_eukarya	SSU rRNA	Eukarya	91	1851	RF01960
SSU_rRNA_microsporidia	SSU rRNA	Euk-Microsporidia	46	1312	RF02542
LSU_rRNA_archaea	LSU rRNA	Archaea	91	2990	RF02540
LSU_rRNA_bacteria	LSU rRNA	Bacteria	102	2925	RF02541
LSU_rRNA_eukarya	LSU rRNA	Eukarya	88	3401	RF02543
SSU_rRNA_mitochondria_metazoa	SSU rRNA	Mito-Metazoa	83	954	–
SSU_rRNA_mitochondria_amoeba	SSU rRNA	Mito-Amoeba	2	1861	–
SSU_rRNA_mitochondria_chlorophyta	SSU rRNA	Mito-Chlorophyta	2	1200	–
SSU_rRNA_mitochondria_fungi	SSU rRNA	Mito-Fungi	4	1603	–
SSU_rRNA_mitochondria_kinetoplast	SSU rRNA	Mito-Kinetoplast	3	624	–
SSU_rRNA_mitochondria_plant	SSU rRNA	Mito-Plant	4	1951	–
SSU_rRNA_mitochondria_protist	SSU rRNA	Mito-Protist	2	1677	–
SSU_rRNA_chloroplast	SSU rRNA	Chloroplast	94	1488	–
SSU_rRNA_chloroplast_pilostyles	SSU rRNA	Chloroplast	1	1531	–
SSU_rRNA_cyanobacteria	SSU rRNA	Bac-Cyanobacteria	49	1487	–
SSU_rRNA_apicoplast	SSU rRNA	Euk-Apicoplast	3	1463	–

’#seqs’ is the number of sequences in the multiple alignment used to build the model. ’length’ is the number of reference model positions. Abbreviations in ’taxonomy group’ column: ’Bac’ is Bacteria, ’Euk’ is Eukarya and ’Mito’ is Mitochondria

ISSN: 1471-2105