Tag: microRNA

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.

miRD – pre-microRNA Detection

miRD

:: DESCRIPTION

miRD is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1436-7. doi: 10.1093/bioinformatics/btr148. Epub 2011 Mar 23.
Prediction of novel pre-microRNAs with high accuracy through boosting and SVM.
Zhang Y1, Yang Y, Zhang H, Jiang X, Xu B, Xue Y, Cao Y, Zhai Q, Zhai Y, Xu M, Cooke HJ, Shi Q.

SimiRa – Identify Coregulation between microRNAs and RNA-binding proteins

SimiRa

:: DESCRIPTION

simiRa is a tool that compares enriched functional categories such as pathways and GO terms.SimiRa searches for miRNAs and RBPs that target the same genes or have similar functional categories.

::DEVELOPER

Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins.
Preusse M, Marr C, Saunders S, Maticzka D, Lickert H, Backofen R, Theis F.
RNA Biol. 2015 Sep 2;12(9):998-1009. doi: 10.1080/15476286.2015.1068496.

MiRmat – Predict mature microRNA from pri-microRNA

MiRmat

:: DESCRIPTION

MiRmat is a software designed to predict mature microRNA from pri-microRNA. This tool can be divided into two parts, one is for predicting Drosha processing site, which is based on energy distribution pattern along primary microRNA’s secondary structure; the other is for predicting Dicer processing site, which is based on precursor microRNA’s structure feature

::DEVELOPER

Bioinformatics Group in Nanjing University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl
  • RNAfold
  • Matlab

:: DOWNLOAD

   MiRmat

:: MORE INFORMATION

Citation

PLoS One. 2012;7(12):e51673. doi: 10.1371/journal.pone.0051673. Epub 2012 Dec 27.
MiRmat: mature microRNA sequence prediction.
He C, Li YX, Zhang G, Gu Z, Yang R, Li J, Lu ZJ, Zhou ZH, Zhang C, Wang J.

GenemiR 1.0 – Unified Search of Mammalian microRNA Target Predictions

GenemiR 1.0

:: DESCRIPTION

The GenemiR software application is a tool aimed at biologists and bioinformaticians who wish to find prediction and expression patterns in sets of microRNAs and genes. The program works with mouse and human target prediction and expression data.

::DEVELOPER

Bertone Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenemiR

:: MORE INFORMATION

miRNAkey 1.2 – Analysis of microRNA Deep Sequencing data

miRNAkey 1.2

:: DESCRIPTION

miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data.

::DEVELOPER

Roy Ronen

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 miRNAkey

:: MORE INFORMATION

Citation

Roy Ronen; Ido Gan; Shira Modai;Alona Sukacheov; Gideon Dror; Eran Halperin; Noam Shomron.
miRNAkey: a software for microRNA Deep Sequencing analysis.
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq493

miRFinder 4.0 – MicroRNA Prediction

miRFinder 4.0

:: DESCRIPTION

MiRFinder is a high throughput and good performance computational pre-miRNA prediction tool. The tool was designed for genome-wise, pair-wise sequences from two related species. In our experiments, the MiRFinder has demontracted reasonably better sensitivity and speed comparing to similar tools.

::DEVELOPER

Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 miRFinder

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Sep 17;8:341.
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
Huang TH, Fan B, Rothschild MF, Hu ZL, Li K, Zhao SH.