User specific sequence

RNAhybrid

Additional Info

  • Activitiy Active
  • Description
    "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.
  • Main feature Hybridization of two RNA sequence
  • Unique features
    Searching the minimum free energy hybridization of two desired RNA sequences
  • Organism Human, Insects, Nematodes
  • Category User defined sequence target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2006
  • Citations per year 42
  • Last update Friday, 14 July 2006
  • Updated over past 3 years No
  • Relative Popularity 31617

miRNA_Targets

Additional Info

  • Activitiy Active
  • Description
    miRNA_Targets implemented well establised miRNA target prediction algorithms miRanda and RNAhybrid on mRNA 5 prime UTR's , coding regions and 3 prime UTR's. MicroRNA target predictions using 2 algorithms on 7 genomes. Versatile search capabilities using miRNA or mRNA individually or in groups. Gene ontology classification of sets of target genes. Visualization of miRNA and target gene location network on chromosomes.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Interaction prediction of a desired sequence and known miRNAs
    Target prediction using miRanda and RNAhybrid  algorithms on
    mRNA 5´ UTR's , coding regions and 3´ UTR's
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 3.5
  • Last update Saturday, 25 August 2012
  • Updated over past 3 years No
  • Relative Popularity 15618

PITA

Additional Info

  • Activitiy Active
  • Description
    PITA devise a parameter-free model for microRNA-target interaction that computes the difference between the free energy gained from the formation of the microRNA-target duplex and the energetic cost of unpairing the target to make it accessible to the microRNA. This model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Assessment of interactions between RNA sequences based on PITA algorithm
    Using known miRNAs or user-provided miRNA sequences 
  • Organism Human, Mouse, Insects, Nematodes
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2007
  • Citations per year 114.89
  • Last update Sunday, 23 September 2007
  • Updated over past 3 years No
  • Relative Popularity 57269

RNA22 v2

Additional Info

  • Activitiy Active
  • Description
    RNA22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. RNA22 does not rely 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.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Identifying microRNA binding sites and their corresponding heteroduplexes
    Interaction prediction between a desired miRNA and target sequence
  • Organism Human, Mouse, Insects, Nematodes
  • Category User defined sequence target prediction
  • Other covered categories
    Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2006
  • Citations per year 90.4
  • Last update Thursday, 09 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 47227

IntaRNA

Additional Info

  • Activitiy Active
  • Description
    "IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Prediction of interactions between two RNA molecules
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2008
  • Citations per year 18.75
  • Last update Tuesday, 15 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 20164

MIRZA

Additional Info

  • Activitiy Active
  • Description
    MIRZA is a biophysical model of miRNA-target interaction and infer its parameters from Argonaute 2 cross-linking and immunoprecipitation data. We show that a substantial fraction of human miRNA target sites are noncanonical and that predicted target-site affinity correlates well with the extent of target destabilization.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    A biophysical miRNA-mRNA interaction model based on Argonaute 2 cross-linking and immunoprecipitation data
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2013
  • Citations per year 16.67
  • Last update Sunday, 20 January 2013
  • Updated over past 3 years No
  • Relative Popularity 44014

MR-microT

Additional Info

  • Activitiy Active
  • Description
    MR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences. MR-microT offers the highly requested by life scientists feature of predicting the targets of ad-hoc miRNA molecules in near-real time through an intuitive Web interface.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Provides near-real time predictions for custom miRNA sequences
  • Organism Human, Mouse, Insects
  • Category User defined sequence target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2012
  • Citations per year 25.25
  • Last update Monday, 30 June 2014
  • Updated over past 3 years Yes
  • Relative Popularity 579395

psRNATarget

Additional Info

  • Activitiy Active
  • Description
    psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: reverse complementary matching between miRNA and target transcript using a proven scoring schema, and target site accessibility evaluation by calculating unpaired energy required to open secondary structure around miRNA’s target site on mRNA. PsRNATarget distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript
  • Main feature miRNA target prediction
  • Unique features
    Reverse complementary matching between miRNA and target transcript using a proven scoring schema Target site accessibility evaluation by calculating unpaired energy
  • Organism Plants
  • Category User defined sequence target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2011
  • Citations per year 90.4
  • Last update Friday, 01 July 2011
  • Updated over past 3 years No
  • Relative Popularity 335799

TAPIR

Additional Info

  • Activitiy Active
  • Description
    TAPIR is designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools.
  • Main feature miRNA target prediction
  • Unique features
    Search for plant miRNA targets using a fast and a precise algorithm User defined score and free energy ratio
  • Organism Plants
  • Category User defined sequence target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 10
  • Last update Thursday, 29 April 2010
  • Updated over past 3 years Yes
  • Relative Popularity 17611