Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution

BMC Bioinformatics

Table 1 Representative computational methods for RBP binding preference prediction

Method	Input data	Ref	Highlight
DeepBind	RNAcompete	[10]	Learning sequence preference as
			the convolution function in a deep
			convolutional neural network
MEMERIS	SELEX	[13]	Estimating sequence preference
			(PWM) with single-stranded
			structure context by maximum
			likelihood estimation
Li et al.	RIP-chip	[14]	Predicting sequence preference
			(consensus) with single-stranded
			structure context by iterative
			refinement
RNAcontext	RNAcompete	[15]	Learning a joint model with
			PWM for sequence preference
			and probability vector for structure
			preference
GraphProt	CLIP-seq	[16]	Learning sequence and structure
			preference using graph encoding
			and graph-kernel SVM
RCK	RNAcompete	[17]	Extending RNAcontext using
			position-dependent k-mer model
			for sequence and structure
			preference

ISSN: 1471-2105