MDCAP – MiRNA-Disease Causal Association Predictor

MDCAP

:: DESCRIPTION

The MDCAP is a computinal model for predicting novel causal miRNA-disease associations. MDCAP would calculate a score for all potential causal miRNA-disease associations. With the score, users could identify most potential causal miRNAs for a given disease or new causal associated disease of a miRNA.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

MDCAP

:: MORE INFORMATION

Citation

Gao Y, Jia K, Shi J, Zhou Y, Cui Q.
A Computational Model to Predict the Causal miRNAs for Diseases.
Front Genet. 2019 Oct 3;10:935. doi: 10.3389/fgene.2019.00935. PMID: 31632446; PMCID: PMC6786093.

MISIM 2.0 – miRNA Functional Similarity Measuring

MISIM 2.0

:: DESCRIPTION

MISIM is a tool for the miRNA functional similarity measuring and network construction. Given a miRNA list, MISIM measures the pairwise functional similarity of the given miRNAs. MISIM is also able to generate a miRNA functional network according to the calculated MISIM similarity coefficients for given miRNAs.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

MISIM

:: MORE INFORMATION

Citation

Li J, Zhang S, Wan Y, Zhao Y, Shi J, Zhou Y, Cui Q.
MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations.
Nucleic Acids Res. 2019 Jul 2;47(W1):W536-W541. doi: 10.1093/nar/gkz328. PMID: 31069374; PMCID: PMC6602518.

MatureBayes – Web-based tool for the Computational Identification of Mature miRNAs

MatureBayes

:: DESCRIPTION

MatureBayes is a tool for finding mature miRNA within a miRNA precursor sequence using a Naive Bays classifier.

::DEVELOPER

Computational Biology Lab, IMBB/FORTH

: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

MatureBayes

:: MORE INFORMATION

Citation

MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.
Gkirtzou K, Tsamardinos I, Tsakalides P, Poirazi P.
PLoS One. 2010 Aug 6;5(8):e11843. doi: 10.1371/journal.pone.0011843.

MiRduplexSVM – MiRNA-Duplex Prediction and Evaluation Methodology

MiRduplexSVM

:: DESCRIPTION

MiRduplexSVM is the first software to provide precise information about all four ends of the miRNA duplex.

::DEVELOPER

Computational Biology Lab, IMBB/FORTH

: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
MATLAB

:: DOWNLOAD

MiRduplexSVM

:: MORE INFORMATION

Citation

MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology.
Karathanasis N, Tsamardinos I, Poirazi P.
PLoS One. 2015 May 11;10(5):e0126151. doi: 10.1371/journal.pone.0126151.

miRlastic 1.0 – Integrative Analysis of miRNA and mRNA Expression data

miRlastic 1.0

:: DESCRIPTION

miRlastic is a novel method which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.

::DEVELOPER

Computational Cell Maps Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Windows/ Linux
R

:: DOWNLOAD

miRlastic

:: MORE INFORMATION

Citation

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma.
Sass S, Pitea A, Unger K, Hess J, Mueller NS, Theis FJ.
Int J Mol Sci. 2015 Dec 18;16(12):30204-22. doi: 10.3390/ijms161226230.

MirCompare 2.0 – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare 2.0

:: DESCRIPTION

MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.

::DEVELOPER

MirCompare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction.
Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C.
J Comput Biol. 2016 Jul 18.

SurvMicro v0.9 – Assessment of Prognostic miRNA Signatures

SurvMicro v0.9

:: DESCRIPTION

SurvMicro is a free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis.

::DEVELOPER

SurvMicro team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1630-2. doi: 10.1093/bioinformatics/btu087. Epub 2014 Feb 11.
SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis.
Aguirre-Gamboa R, Trevino V.

miRPredictor – miRNA Target Predictor based on Support Vector Machine

miRPredictor

:: DESCRIPTION

miRPredictor is a novel miRNA target predictor which is based on support vector machine (SVM), a widely-used machine learning approach, combined with feature selection procedure. We considered different types of features including the flanking sequences of the potential targets and pattern information. The features selected were also analyzed to dig out the intrinsic mechanism of miRNA-target interaction.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
Perl

:: DOWNLOAD

miRPredictor

:: MORE INFORMATION

miRSystem 20160511 – miRNA integrated System for Target Genes Prediction

miRSystem 20160511

:: DESCRIPTION

MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. miRSystem integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan.

::DEVELOPER

Bioinformatics and Biostatistics Core,NTU Center of Genomic Medicine,National Taiwan University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PLoS One. 2012;7(8):e42390. doi: 10.1371/journal.pone.0042390. Epub 2012 Aug 1.
miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
Lu TP1, Lee CY, Tsai MH, Chiu YC, Hsiao CK, Lai LC, Chuang EY.

MiRNA Profiling 0.2.8 – Profile Content of miRNA Sequencing Run

MiRNA Profiling 0.2.8

:: DESCRIPTION

MiRNA Profiling is a software to profile the content of a miRNA sequencing run.Given a set of aligned reads in 1 or more .sam files, produce an annotated version of the .sam where each read is given an annotation based on its coordinate. Additional summary information about the content of each sample is also generated, including miRNA species and other genomic features found.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: REQUIREMENTS

Linux

:: DOWNLOAD

MiRNA Profiling

:: MORE INFORMATION

Based on analysis software used in Morin et al.,
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.,
Genome Res. 2008.18: 610-621