An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

Table 1 Statistics of types of functional RNA motifs supported in RegRNA 2.0

Types of functional RNA motifs	Incorporated data	Incorporated approaches	Number of entries
Splicing sites		GeneSplicer [15]
Splicing regulatory motifs	AEdb [8]	RegRNA 2.0	294 splicing motifs
Polyadenylation Sites		polya_svm [16]
Ribosome binding site		RBSfinder [17]
Rho-independent terminator		TransTermHP [18]
UTR Motifs	UTRsite [1]	PatSearch [22]	48 UTRsite motifs
AU-rich element	ARED [10]	RegRNA 2.0	5 ARE patterns
RNA editing sites		CURE [19]
Riboswitches	RiboSW models	RiboSW [21]	12 riboswitches
RNA elements	ERPIN profiles	ERPIN [23]	11 RNA elements
RNA cis-regulatory elements	Rfam CMs [4]	INFERNAL [24]	209 Rfam cis-reg families
Long stem		einverted [30]
Known functional RNAs	fRNAdb [7]	BLAST [29]	475,318 fRNAdb sequences
miRNA target	miRBase [28]	miRanda [20]	21,643 miRNA sequences
ncRNA hybridization sites	NONCODE [11]	BLAST [29], RNAcofold [34]	170,581 ncRNA sequences
TRANSFAC motifs	TRANSFAC [14]	Match [25]	2,171 transcription factor binding matrices
User-defined motif		RNAMotif [26]
Open Reading Frame		RegRNA 2.0
GC-content ratio		RegRNA 2.0
RNA accessibility		RNAplfold [34]

ISSN: 1471-2105