mimiRNA – microRNA Expression Profiler

mimiRNA

:: DESCRIPTION

mimiRNA is an online resource that integrates expression data from 1483 samples and permits visualization of the expression of 635 human miRNAs across 188 different tissues or cell types.

::DEVELOPER

Centenary Institute – Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ritchie W, Flamant S, Rasko JE.
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets.
Bioinformatics. 2010 Jan 15;26(2):223-7. doi: 10.1093/bioinformatics/btp649. Epub 2009 Nov 17. PMID: 19933167.

miREval 2.0 – microRNA Prediction in Genome Sequences

miREval 2.0

:: DESCRIPTION

miREval is an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms.

::DEVELOPER

Centenary Institute – Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Gao D, Middleton R, Rasko JE, Ritchie W.
miREval 2.0: a web tool for simple microRNA prediction in genome sequences.
Bioinformatics. 2013 Dec 15;29(24):3225-6. doi: 10.1093/bioinformatics/btt545. Epub 2013 Sep 18. PMID: 24048357; PMCID: PMC5994938.

MicroSNiPer – Prediction of SNP effects on putative microRNA targets

MicroSNiPer

:: DESCRIPTION

MicroSNiPer is a web-based application which predicts the impact of a SNP on putative microRNA targets.

::DEVELOPER

Bioinformatics and Next Generation Sequencing Group; Max Planck Institute of Immunobiology and Epigenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7.
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets.
Barenboim M1, Zoltick BJ, Guo Y, Weinberger DR.

MiRGator 3.0 – microRNA portal in Deep Sequencing era

MiRGator 3.0

:: DESCRIPTION

miRGator aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools.

::DEVELOPER

Ewha Research Center for Systems Biology (ERCSB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan;41(Database issue):D252-7. doi: 10.1093/nar/gks1168. Epub 2012 Nov 27.
MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting.
Cho S1, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Chang H, Ryu D, Lee B, Kim VN, Kim W, Lee S.

IMMP – Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA

IMMP

:: DESCRIPTION

IMMP explores two approaches for the investigation of gene-miRNA relationships by integrating mRNA expression and protein expression data. It presents ranked miRNAs lists according to their effects on cancer development and constructed modules containing mRNAs, proteins, and miRNAs, in which these three molecular types are highly correlated.

::DEVELOPER

Data Mining & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

IMMP

:: MORE INFORMATION

Citation

Seo J, Jin D, Choi CH, Lee H.
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs.
PLoS One. 2017 Jan 5;12(1):e0168412. doi: 10.1371/journal.pone.0168412. PMID: 28056026; PMCID: PMC5215789.

MiRTif – MicroRNA:Target Interaction Filter

MiRTif

:: DESCRIPTION

MiRTif is a machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRandaPicTar and TargetScanS.

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MiRTif: a support vector machine-based microRNA target interaction filter.
Yang Y, Wang YP, Li KB.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S4. doi: 10.1186/1471-2105-9-S12-S4.

PARma 1.0 – PAR-CLIP data microRNA Assignment

PARma 1.0

:: DESCRIPTION

PAR-CLIP is a high-throughput method to identify binding sites of RNA binding proteins.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 PAR-CLIP

:: MORE INFORMATION

Citation

PARma: identification of microRNA target sites in Argonaute PAR-CLIP data.
Erhard F, Dolken L, Jaskiewicz L, Zimmer R.
Genome Biol. 2013 Jul 29;14(7):R79.
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iMiRNA-PseDPC – microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach

iMiRNA-PseDPC

:: DESCRIPTION

The web-server iMiRNA-PseDPC was developed for identifying the real microRNA precursors and false microRNA precursors.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2015 Feb 3:1-28. [Epub ahead of print]
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach.
Liu B1, Fang L, Liu F, Wang X, Chou KC.

miRNA-deKmer – Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

miRNA-deKmer

:: DESCRIPTION

miRNA-deKmer is a web server of identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.
Liu B, Fang L, Wang S, Wang X, Li H, Chou KC.
J Theor Biol. 2015 Nov 21;385:153-9. doi: 10.1016/j.jtbi.2015.08.025.

iMcRNA / miRNA-dis – microRNA Precursor Identification based on Distance Structure Status Pairs

 iMcRNA / miRNA-dis

:: DESCRIPTION

The web-server iMcRNA was developed for identifying the real microRNA precursors and false microRNA precursors.

miRNA-dis: microRNA precursor identification based on distance structure status pairs

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Identification of real microRNA precursors with a pseudo structure status composition approach.
Liu B, Fang L, Liu F, Wang X, Chen J, Chou KC.
PLoS One. 2015 Mar 30;10(3):e0121501. doi: 10.1371/journal.pone.0121501.

Mol Biosyst. 2015 Apr;11(4):1194-204. doi: 10.1039/c5mb00050e.
miRNA-dis: microRNA precursor identification based on distance structure status pairs.
Liu B1, Fang L, Chen J, Liu F, Wang X.