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.

TargetRank 1.0 – Rank Conserved and non-conserved microRNA Targets and siRNA off-targets

TargetRank 1.0

:: DESCRIPTION

 TargetRank is a webtool for ranking conserved and non-conserved microRNA targets and siRNA off-targets.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007).
Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs.
RNA 13, 1894-1910.

Chimira 1.5 – Analysis of small RNA Sequencing data and microRNA modifications

Chimira 1.5

:: DESCRIPTION

Chimira is an online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile.

::DEVELOPER

Chimira team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Chimira: Analysis of small RNA Sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics. 2015 Jun 20. pii: btv380.

ProteoMirExpress – Inferring microRNA and Protein-centered Regulatory Networks

ProteoMirExpress

:: DESCRIPTION

ProteoMirExpress is a web server that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browsesr

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2013 Nov;12(11):3379-87. doi: 10.1074/mcp.O112.019851. Epub 2013 Aug 7.
ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data.
Qin J1, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J.

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.