Tools4miRs - Target Prediction - Target Prediction Meta-Server

Target Prediction Meta-Server
Comprehensive service to compute and collect data from various target prediction tools

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Number of tools found: 10

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	#	Name	Description	Online/Local	Organism Specific	Algorithm Features	Target Region	References
	1	GUUGle	GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.	/	any	seed match G:U pairs allowed in the seed	any	Homepage Publication Jan. 10, 2006 Citations: 23
	2	MicroTar	MicroTar is a microRNA target prediction program based on mRNA sequence complementarity (3'-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA molecules. It uses the RNAlib library from the Vienna RNA package	/	animals	seed match free energy site accessibility G:U pairs allowed in the seed	3' UTR	Homepage Publication Dec. 18, 2006 Citations: 44
	3	miRanda	miRanda algorithm is based on a comparisone of miRNAs complementarity to 3'UTR regions. The binding energy of the duplex structure, evolutionary conservation of the whole target site and its position within 3”UTR are calculated and account for a final result which is a weighted soum of match and mismatch scores for base pairs and gap penalties.	/	any	seed match conservation free energy G:U pairs allowed in the seed	3' UTR, CDS	Homepage Publication Oct. 5, 2004 Citations: 1807
	4	miRmap	To evaluate the strenght of the resulting mRNA repression, the miRNA taregt predictors may employ thermodynamic, evolutionary, probabilistic, or sequence-based features. An open source software library, miRmap, for the first time comprehensively covers all four approaches using eleven predictor features, three of which are novel. Overall, target site accessibility appears to be the most predictive feature. Moreover novel feature based on PhyloP, which evaluates the significance of negative selection, is the best performing predictor in the evolutionary category.	/	human mouse rat cow chicken zebrafish other animals (selectable)	seed match conservation free energy site accessibility local AU content Site over-representation probability	3'UTR	Homepage Publication May 28, 2013 Citations: 73
	5	PITA	PITA offers a brand new view on the miRNA target prediction. The main assumption is based on the fact the mRNA structure plays a role in target recognition by thermodynamically promoting or disfavoring the interaction.	/	human (online) fly (online) mouse (online) worm (online) animals (local)	seed match free energy site accessibility target-site abundance G:U pairs allowed in the seed	3' UTR	Homepage Publication Sept. 23, 2007 Citations: 1252
	6	psRobot	psRobot is designed to analyze batch of plant small RNA data.The online version of psRobot has two modules. The stem-loop small RNA prediction module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences. The second one, small RNA target prediction module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants.	/	plants	seed match conservation target-site abundance 3' compensatory pairing G:U pairs allowed in the seed	any	Homepage Publication June 12, 2012 Citations: 246
	7	RNA22	Rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not relay upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA.	/	animals	seed match free energy G:U pairs allowed in the seed sensitivity/specificity settings pattern recognision	any	Homepage Publication July 26, 2006 Citations: 992
	8	RNAhybrid	RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.	/	any	seed match free energy target-site abundance 3' compensatory pairing G:U pairs allowed in the seed	3' UTR	Homepage Publication July 1, 2006 Citations: 904
	9	Target-align	A Smith-Waterman-like alignment tool was developed in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace the optimal local alignments. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings.	/	plants	seed match 3' compensatory pairing G:U pairs allowed in the seed	any	Homepage Publication Oct. 7, 2010 Citations: 31
	10	TargetSpy	TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. It does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.	/	human mouse chicken rat fly	free energy site accessibility machine learning 3' compensatory pairing	3' UTR	Homepage Publication May 28, 2010 Citations: 76