Tag: miRNA

miRbiom – A Machine Learning Approach to Profile miRNAs

miRbiom

:: DESCRIPTION

miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles

::DEVELOPER

SCBB-LAB (Studio of Computational Biology and Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

miRbiom

:: MORE INFORMATION

Citation

Pradhan UK, Sharma NK, Kumar P, Kumar A, Gupta S, Shankar R.
miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.
PLoS One. 2021 Oct 12;16(10):e0258550. doi: 10.1371/journal.pone.0258550. PMID: 34637468; PMCID: PMC8509996.

miRPara 6.3 – SVM-based miRNA Prediction tool

miRPara 6.3

:: DESCRIPTION

miRPara predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine (SVM) to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set.

::DEVELOPER

miRPara team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRPara

:: MORE INFORMATION

Citation:

Wu Y., Wei B., Liu H., Li T., Rayner S.
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
BMC Bioinformatics. 2011 Apr 19; 12(1):107

iwa-miRNA – Interactive Annotation of Plant MiRNAs

iwa-miRNA

:: DESCRIPTION

iwa-miRNA is a web-based platform for interactive annotation of plant miRNAs.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

iwa-miRNA 

:: MORE INFORMATION

Citation

Zhang T, Zhai J, Zhang X, Ling L, Li M, Xie S, Song M, Ma C.
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.
Genomics Proteomics Bioinformatics. 2021 Jul 28:S1672-0229(21)00161-3. doi: 10.1016/j.gpb.2021.02.010. Epub ahead of print. PMID: 34332120.

PROmiRNA v2 – Annotating miRNA Promoters in Human

PROmiRNA v2

:: DESCRIPTION

PROmiRNA is a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features.

::DEVELOPER

PROmiRNA team , Max Planck Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python

:: DOWNLOAD

 PROmiRNA

:: MORE INFORMATION

Citation

Genome Biol. 2013 Aug 16;14(8):R84. [Epub ahead of print]
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.
Marsico A1, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom UA, Vingron M.

miRNAmRNA 1.0 – miRNA mRNA Expression Integration

miRNAmRNA 1.0

:: DESCRIPTION

miRNAmRNA: Integrated analysis of microRNA and mRNA

::DEVELOPER

Maarten van Iterson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 miRNAmRNA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(15):e146. doi: 10.1093/nar/gkt525. Epub 2013 Jun 14.
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions.
van Iterson M1, Bervoets S, de Meijer EJ, Buermans HP, ‘t Hoen PA, Menezes RX, Boer JM.

TargetProfiler – miRNA Target Prediction tool

TargetProfiler

:: DESCRIPTION

Targetprofiler is a novel miRNA target prediction tool that utilizes a probabilistic learning algorithm in the form of a hidden Markov model trained on experimentally verified miRNA targets.

::DEVELOPER

Ioannis Iliopoulos’ Bioinformatics & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNA Biol. 2012 Sep;9(9):1196-207. doi: 10.4161/rna.21725. Epub 2012 Sep 1.
A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2.
Oulas A1, Karathanasis N, Louloupi A, Iliopoulos I, Kalantidis K, Poirazi P.

SSCprofiler – miRNA Gene Prediction

SSCprofiler

:: DESCRIPTION

SSCprofiler (Sequence, Structure and Conservation) is a new computational tool utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors.

::DEVELOPER

Ioannis Iliopoulos’ Bioinformatics & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jun;37(10):3276-87. doi: 10.1093/nar/gkp120. Epub 2009 Mar 25.
Prediction of novel microRNA genes in cancer-associated genomic regions–a combined computational and experimental approach.
Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P.

miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

BioVLAB-MMIA-NGS – miRNA mRNA Integrated Analysis

BioVLAB-MMIA-NGS

:: DESCRIPTION

BioVLAB-MMIA-NGS is a reconfigurable cloud computing environment for microRNA and mRNA integrated analysis using sequencing data

::DEVELOPER

B&H (Bio and Health Informatics) lab , SNU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioVLAB-MMIA-NGS

 :: MORE INFORMATION

Citation

BioVLAB-MMIA-NGS: MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data.
Chae H, Rhee S, Nephew KP, Kim S.
Bioinformatics. 2014 Sep 29. pii: btu614.

BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.
Lee H, Yang Y, Chae H, Nam S, Choi D, Tangchaisin P, Herath C, Marru S, Nephew KP, Kim S.
IEEE Trans Nanobioscience. 2012 Sep;11(3):266-72. doi: 10.1109/TNB.2012.2212030.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. doi: 10.1093/nar/gkp294. Epub 2009 May 6.
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression.
Nam S1, Li M, Choi K, Balch C, Kim S, Nephew KP.

miRPlant v6 – An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data

miRPlant v6

:: DESCRIPTION

miRPlant extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants.

::DEVELOPER

miRPlant team

:: SCREENSHOTS

miRPlant

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 miRPlant

:: MORE INFORMATION

Citation

An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC:
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.
BMC bioinformatics 2014, 15(1):275.