Tag: microRNA

miRDeep-P 1.3 / miRDP2 1.1.5 – Analyzing the microRNA Transcriptome in Plants

miRDeep-P 1.3 / miRDP2 1.1.5

:: DESCRIPTION

miRDeep-P (miRDP)  is a tool which can be used to detecting miRNAs in plants from deeply sequenced small RNA libraries. It was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria.

miRDP2 is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm.

::DEVELOPER

Yang lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 miRDeep-P / miRDP2 

:: MORE INFORMATION

Citation

Kuang Z, Wang Y, Li L, Yang X.
miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.
Bioinformatics. 2019 Jul 15;35(14):2521-2522. doi: 10.1093/bioinformatics/bty972. PMID: 30521000.

Bioinformatics. 2011 Sep 15;27(18):2614-5. doi: 10.1093/bioinformatics/btr430. Epub 2011 Jul 19.
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
Yang X1, Li L.

miRNAminer – microRNA Homology Search

miRNAminer

:: DESCRIPTION

miRNAminer is a web-based tool used for homologous miRNA gene search in several species. Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity.

::DEVELOPER

Adam Kiezun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Jan 23;9:39. doi: 10.1186/1471-2105-9-39.
miRNAminer: a tool for homologous microRNA gene search.
Artzi S1, Kiezun A, Shomron N.

miRviewer – Multispecies microRNA Homologous Viewer

miRviewer

:: DESCRIPTION

microRNAviewer presents a global view of homologous miRNA genes in many species.

::DEVELOPER

miRviewer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Res Notes. 2012 Feb 13;5:92. doi: 10.1186/1756-0500-5-92.
miRviewer: a multispecies microRNA homologous viewer.
Kiezun A1, Artzi S, Modai S, Volk N, Isakov O, Shomron N.

MixMir – Mixed linear models for microRNA Motif Finding

MixMir

:: DESCRIPTION

MixMir is a program for finding microRNA motifs using gene expression and 3′ UTR sequence data.

::DEVELOPER

Kevin Chen’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MixMir

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014;42(17):e135. doi: 10.1093/nar/gku672. Epub 2014 Jul 31.
MixMir: microRNA motif discovery from gene expression data using mixed linear models.
Diao L, Marcais A, Norton S, Chen KC

mirnaDetect – Predict possible microRNA Precursors within Genome data

mirnaDetect

:: DESCRIPTION

A java based mining tool mirnaDetect is developed for detect potential pre-miRNAs from the genome-scale data. This program is based both on search and machine learning algorithms.

::DEVELOPER

Leyi Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 mirnaDetect

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov 8.
Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set.
Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q.

miR-PREFeR 0.24 – microRNA PREdiction From small RNA-seq data

miR-PREFeR 0.24

:: DESCRIPTION

miR-PREFeR uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

::DEVELOPER

Dr. Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 miR-PREFeR

:: MORE INFORMATION

Citation

miR-PREFeR: an accurate, fast, and easy-to-use plant miRNA prediction tool using small RNA-Seq data.
Lei J, Sun Y.
Bioinformatics. 2014 Jun 14. pii: btu380.

TargetMiner – microRNA Target Prediction

TargetMiner

:: DESCRIPTION

TargetMiner is a software to find information about microRNA target mRNA. The classifier Support Vector Machine (SVM) is used to classify the test data. The SVM is trained with a set of biologically validated positive (miRNA- target pairs) and newly generated negative examples (miRNA- non target pairs). A set of 90 targeting site context specific features is then extracted from the training examples. From this a set of 30 most favorable features with high F-Score is then selected to train the classifier.

::DEVELOPER

TargetMiner Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TargetMiner

:: MORE INFORMATION

Citation

Sanghamitra Bandyopadhyay and Ramkrishna Mitra,
“Targetminer:MicroRNA Target Prediction with Systematic Identification Of Tissue Specific Negative Examples“,
Bioinformatics, Vol. 25, no. 20, pp. 2625 – 2631, 2009.

MBSTAR – microRNA Binding Site Prediction tool

MBSTAR

:: DESCRIPTION

MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets) is a web server for accurate prediction of true or functional miRNA binding sites.

::DEVELOPER

Bioinformatics Lab (MIU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MBSTAR

:: MORE INFORMATION

Citation

Sci Rep. 2015 Jan 23;5:8004. doi: 10.1038/srep08004.
MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.
Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z

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.