miRComp – Composite MicroRNA Target Prediction

miRComp

:: DESCRIPTION

miRComp is a filtering step of putative microRNA targets through aggregating the predictions by several algorithms using two composite statistics – composite ranks and composite “p-values”

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRComp

:: MORE INFORMATION

Citation

Jin Zhou, Shili Lin, Vince Melfi, Joe Verducci (2006).
Composite MicroRNA Target Predictions and Comparisons of Several Prediction Algorithms.
MBI Technical Report No. 51.

homoTarget – Prediction of microRNA targets in Homo Sapiens

homoTarget

:: DESCRIPTION

HomoTarget is a new algorithm for prediction of microRNA targets in Homo sapiens.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

HomoTarget

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 HomoTarget

:: MORE INFORMATION

Citation:

Genomics. 2012 Nov 19. pii: S0888-7543(12)00213-3. doi: 10.1016/j.ygeno.2012.11.005. [Epub ahead of print]
HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens.
Ahmadi H1, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A

BosFinder – pre-microRNA Gene prediction algorithm in Bos taurus

BosFinder

:: DESCRIPTION

BosFinder is a new algorithm which was developed to identify and annotate the whole genome’s derived pre-miRNAs.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

BosFinder

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BosFinder

:: MORE INFORMATION

Citation

Anim Genet. 2014 May 17. doi: 10.1111/age.12170. [Epub ahead of print]
BosFinder: a novell pre-microRNA gene prediction algorithm in Bos taurus.
Sadeghi B1, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A.

TarPmiR – microRNA Target Site Prediction

TarPmiR

:: DESCRIPTION

TarPmiR is a miRNA-mRNA binding sites prediction tool, which can utilize miRNA-mRNA binding experiment data such as CLASH (cross-linking ligation and sequencing of hybrids) .

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Python

:: DOWNLOAD

 TarPmiR

:: MORE INFORMATION

Citation:

TarPmiR: a new approach for microRNA target site prediction.
Ding J, Li X, Hu H.
Bioinformatics. 2016 May 20. pii: btw318.

WMD 3.2 – Web MicroRNA Designer

WMD 3.2

:: DESCRIPTION

WMD3 is a web app for the automated design of artificial microRNAs.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • Perl
  • gcc
  • MySQL
  • GenomeMapperBlast,
  • ViennaRNA

:: DOWNLOAD

 WMD

:: MORE INFORMATION

Citation

Plant Cell. 2006 May;18(5):1121-33. Epub 2006 Mar 10.
Highly specific gene silencing by artificial microRNAs in Arabidopsis.
Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D.

miRNAgFree – microRNA prediction using sRNAseq/miRNAseq/sncRNAseq

miRNAgFree

:: DESCRIPTION

miRNAgFree is a novel microRNA prediction approach based on biogenesis features, such as the known 5’ homogeneity, and duplex mean free energies which does not require a genome assembly.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VirtualBox.

:: DOWNLOAD

miRNAgFree

:: MORE INFORMATION

 

spongeScan – Detecting microRNA Binding Elements in lncRNA Sequences

spongeScan

:: DESCRIPTION

spongeScan is a web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.
Nucleic Acids Res. 2016 May 19. pii: gkw443.

MiRPlex 0.1 – microRNA Prediction from High-throughput Sequencing data

MiRPlex 0.1

:: DESCRIPTION

MiRPlex is a tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

 MiRPlex

:: MORE INFORMATION

Citation

Mapleson, D.; Moxon, S.; Dalmay, T.; Moulton, V.,
MirPlex: A tool for identifying miRNAs in high-throughput sRNA datasets without a genome.
J Exp Zool B Mol Dev Evol. 2013 Jan;320(1):47-56. doi: 10.1002/jez.b.22483. Epub 2012 Nov 26.

TargetScore 1.24.0 – Infer microRNA Targets using microRNA-overexpression data and Sequence Information

TargetScore 1.24.0

:: DESCRIPTION

TargetScore: a probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 TargetScore

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):621-8. doi: 10.1093/bioinformatics/btt599. Epub 2013 Oct 17.
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information.
Li Y1, Goldenberg A, Wong KC, Zhang Z.