RScan: fast searching structural similarities for structured RNAs in large databases

BMC Genomics

Table 8 Search more RNA sequences in Rfam seed structural database

Rfam ID of Query	Parameters¹				Hits/ST/F5²	T_search (s)	Mp³	QL⁴
	k	Mc	Id	Ar
RF00009/AF004373.1/1-320	9	27	80	95	1/1/1	10	0.426	320
RF00048/AF405669.1/4445-4505	7	21	90	95	4/3/3	3	0.013	61
RF00167/AL591981.1/205922-205823	7	21	90	95	3/3/3	41	0.140	100
RF00175/AF042101.1/695-812	7	21	90	95	64/64/5	44	0.205	118
RF00181/AL132709.5/131508-131439	7	21	90	95	5/5/5	6	0.886	70
RF00229/AY184219.1/389-639	9	27	80	95	21/21/5	35	0.314	251
RF00342/AP001273.4/3902-3830	7	21	90	95	6/5/5	4	0.013	73
RF00376/AY451114.1/148-231	7	21	90	95	248/248/5	22	0.013	84
RF00436/AL591676.10/16205-16259	7	21	90	95	31/2/2	27	0.062	55
RF00480/AY455785.1/1517-1568	7	21	90	95	453/427/5	10	0.025	52

¹Mc: match-core; Id: identity ≥ %; Ar: Alignment ratio ≥ %.
²ST: number of same type of ncRNA with the query; F5: number of same type ncRNA in first 5 hits.
³Mp: p-value of minimum free energy of queries' predicted secondary structures.
⁴QL: length of query.

ISSN: 1471-2164