Target Prediction Meta-Server

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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: 13
    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: 28
    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: 1155
    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: 15
    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: 822
    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: 63
    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: 612
    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: 361
    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: 23
    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: 45