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.

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

spongeScan team

:: 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.

RNA22 v2 – microRNA Target Detection

RNA22 v2

:: DESCRIPTION

RNA22 finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

RNA 22 full set of predictions  Batch submission tool

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 15;28(24):3322-3. doi: 10.1093/bioinformatics/bts615. Epub 2012 Oct 16.
Interactive exploration of RNA22 microRNA target predictions.
Loher P1, Rigoutsos I.

ChemiRs – Web Server for microRNAs and Chemicals

ChemiRs

:: DESCRIPTION

ChemiRs is a creditable online web server for predicting interactions and relations among miRNAs, chemicals and pathways.

::DEVELOPER

NTNU BISBE

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChemiRs: a web application for microRNAs and chemicals.
Su EC, Chen YS, Tien YC, Liu J, Ho BC, Yu SL, Singh S.
BMC Bioinformatics. 2016 Apr 18;17(1):167. doi: 10.1186/s12859-016-1002-0.

miRQuest – Integration of tools on a Web Server for microRNA Research

miRQuest

:: DESCRIPTION

miRQuest is a webserver that enables to the end-user a friendly and standardized software to use the many ab initio tools for miRNA investigation.

::DEVELOPER

miRQuest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRQuest: integration of tools on a Web server for microRNA research.
Aguiar RR, Ambrosio LA, Sepúlveda-Hermosilla G, Maracaja-Coutinho V, Paschoal AR.
Genet Mol Res. 2016 Mar 28;15(1). doi: 10.4238/gmr.15016861.

MIRUMIR – microRNA as Biomarker In Cancer

MIRUMIR

:: DESCRIPTION

MIRUMIR is an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets.

::DEVELOPER

MIRUMIR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MIRUMIR: an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets.
Antonov AV, Knight RA, Melino G, Barlev NA, Tsvetkov PO.
Cell Death Differ. 2013 Feb;20(2):367. doi: 10.1038/cdd.2012.137

miRNACon – Influence of Confounding Factors Age and Sex on microRNA

miRNACon

:: DESCRIPTION

miRNACon is a web-based application to test individual miRNAs or miRNA signatures for their likelihood of being influenced.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Clin Chem. 2014 Sep;60(9):1200-8. doi: 10.1373/clinchem.2014.224238. Epub 2014 Jun 30.
Influence of the confounding factors age and sex on microRNA profiles from peripheral blood.
Meder B1, Backes C, Haas J, Leidinger P, Stähler C, Großmann T, Vogel B, Frese K, Giannitsis E, Katus HA, Meese E, Keller A.

iMiRNA-SSF – Identification of MicroRNA based on Structure and Sequence Features

iMiRNA-SSF

:: DESCRIPTION

iMiRNA-SSF is a web-server which is a SVM-based online predictor using structure and sequence features for microRNA identification.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions.
Chen J, Wang X, Liu B.
Sci Rep. 2016 Jan 12;6:19062. doi: 10.1038/srep19062.

TargetS – microRNA Target Prediction in Different Gene Regions

TargetS

:: DESCRIPTION

TargetS is a novel computational approach for predicting miRNA targets with the target sites located along entire gene sequences, which permits finding additional targets that are not located in the 3′ un-translated regions.

::DEVELOPER

Yin Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python

:: DOWNLOAD

 TargetS

:: MORE INFORMATION

Citation

Identifying microRNA targets in different gene regions.
Xu W, San Lucas A, Wang Z, Liu Y.
BMC Bioinformatics. 2014;15 Suppl 7:S4. doi: 10.1186/1471-2105-15-S7-S4.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.