miRmap 1.1 / miRmap web – Comprehensive Prediction of microRNA Target Repression Strength

miRmap 1.1 / miRmap web

:: DESCRIPTION

The miRmap library is a Python library predicting the repression strength of microRNA (miRNA) targets.

miRmap web application offers a user-friendly and feature-rich resource for browsing precomputed miRNA target predictions for model organisms, as well as for predicting and ranking targets for user-submitted sequences.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

miRmap

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Dec;40(22):11673-83. doi: 10.1093/nar/gks901. Epub 2012 Oct 2.
MiRmap: comprehensive prediction of microRNA target repression strength.
Vejnar CE1, Zdobnov EM.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W165-8. doi: 10.1093/nar/gkt430. Epub 2013 May 28.
miRmap web: Comprehensive microRNA target prediction online.
Vejnar CE1, Blum M, Zdobnov EM.

miRNALasso – microRNA Target Prediction

miRNALasso

:: DESCRIPTION

miRNALasso is a adaptive Lasso based method that integrates full spectrum of sequence features for microRNA target prediction.

::DEVELOPER

the Liu Lab , The UT Health Science Center at Houston.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
MatLab

:: DOWNLOAD

miRNALasso

:: MORE INFORMATION

Citation

Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions.
Wang Z, Xu W, Liu Y.
Bioinformatics. 2015 Jun 30. pii: btv392.

TargetScan 7.2 – Prediction of microRNA Targets

TargetScan 7.2

:: DESCRIPTION

TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA (ref. 1). As an option, nonconserved sites are also predicted.`

::DEVELOPER

Bioinformatics and Research Computing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Lewis, B. P., Shih, I-h., Jones-Rhoades, M. W., Bartel, D. P. and Burge, C. B. (2003).
Prediction of mammalian microRNA targets.
Cell 115, 787-798. (TargetScan)

Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005).
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
Cell 120, 15-20. (TargetScanS)

RAmiRNA – Viral mature MicroRNA prediction Toolkit

RAmiRNA

:: DESCRIPTION

RAmiRNA (RAdicalmiRNA detector) is a software to solve the problem of custom development of prediction models for mature miRNAs using support vector machine (SVM) learning.

::DEVELOPER

Indo-Russian Centre for Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RAmiRNA

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(12):581-5. doi: 10.6026/97320630008581. Epub 2012 Jun 28.
RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs.
Tyagi V, Prasad CS.

miTRATA v1.3 – microRNA Truncation and Tailing Analysis

miTRATA v1.3

:: DESCRIPTION

miTRATA is a web-based tool for microRNA Truncation and Tailing Analysis – the analysis of 3′ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence.

::DEVELOPER

the Meyers lab at the University of Delaware.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

miTRATA

:: MORE INFORMATION

Citation

miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.
Patel P, Ramachandruni SD, Kakrana A, Nakano M, Meyers BC.
Bioinformatics. 2015 Oct 10. pii: btv583.

TargetSpy 1.0 – microRNA Target Prediction

TargetSpy 1.0

:: DESCRIPTION

TargetSpy is a novel computational approach for predicting target sites regardless of the presence of a seed match.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java

:: DOWNLOAD

TargetSpy

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 28;11:292. doi: 10.1186/1471-2105-11-292.
TargetSpy: a supervised machine learning approach for microRNA target prediction.
Sturm M1, Hackenberg M, Langenberger D, Frishman D.

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.

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.

miRanda 1.9 – microRNA Target Detection Software

miRanda 1.9

:: DESCRIPTION

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. miRanda reads RNA sequences (such as microRNAs) from file1 and genomic DNA/RNA sequences from file2. Both of these files should be in FASTA format.

::DEVELOPER

the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

miRanda

:: MORE INFORMATION

Citation

John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS.,
Human MicroRNA Targets
PLoS Biol. 2005 Jul;3(7):e264.

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

:: DOWNLOAD

:: 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.