MultiMiTar – Predict mRNA Targets of a Given microRNA

MultiMiTar

:: DESCRIPTION

MultiMiTar is an enhancement of TargetMiner with multiobjective feature selection and ranking of the predicted mRNA targets of a given microRNA

::DEVELOPER

Bioinformatics Lab at Machine Intelligence Uni

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MultiMiTar

:: MORE INFORMATION

Citation

Ramkrishna Mitra and Sanghamitra Bandyopadhyay,
“MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method“,
PLoS ONE 6(9): e24583. doi:10.1371/journal.pone.0024583.

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.

CRISPRTarget – A Tool to Explore Targets of CRISPR RNAs

CRISPRTarget

:: DESCRIPTION

CRISPRTarget predicts the most likely targets of CRISPR RNAs

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

RNA Biol. 2013 May;10(5):817-27. doi: 10.4161/rna.24046. Epub 2013 Mar 14.
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
Biswas A1, Gagnon JN, Brouns SJ, Fineran PC, Brown CM.

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)

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.

sPARTA 1.27 – small RNA-PARE Target Analyzer

sPARTA 1.27

:: DESCRIPTION

sPARTA is a high performance software for the validation of plant miRNA or sRNA targets with PARE (Parallel Analysis of Read Ends) data.

::DEVELOPER

Atul Kakrana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

sPARTA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct;42(18):e139. doi: 10.1093/nar/gku693. Epub 2014 Aug 12.
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC

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.

TARGeT 2.10 – Tree Analysis of Related Genes and Transposons

TARGeT 2.10

:: DESCRIPTION

TARGeT (Tree Analysis of Related Genes and Transposons) uses either a DNA or amino acid ‘seed’ query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs).

::DEVELOPER

TARGet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Yujun Han, James M. Burnette III and Susan R. Wessler
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
Nucl. Acids Res. (2009) 37 (11): e78.

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.