HHMMiR 1.2 – Prediction of microRNAs using Hierarchical Hidden Markov models

HHMMiR 1.2

:: DESCRIPTION

HHMMiR is a novel approach for de novo miRNA hairpin prediction in the absence of evolutionary conservation. HHMMiR implements a Hierarchical Hidden Markov Model (HHMM) that utilizes region-based structural as well as sequence information of miRNA precursors.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HHMMiR

:: MORE INFORMATION

Citation:

S. Kadri, V. Hinman, P.V. Benos,
HHMMiR: Efficient de novo Prediction of MicroRNAs using Hierarchical Hidden Markov Models“,
BMC Bioinformatics (Proc APBC 2009) (2009) 10 (Suppl 1):S35.

mirConnX – Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks

mirConnX

:: DESCRIPTION

mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.

Treebic 1.11 – Hierarchical Generative Biclustering for MicroRNA Expression Analysis

Treebic 1.11

:: DESCRIPTION

Treebic is a Software package for hierarchical biclustering.

::DEVELOPER

Probabilistic Machine Learning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

 Treebic

:: MORE INFORMATION

Citation

J. Caldas and S. Kaski.
Hierarchical generative biclustering for microRNA expression analysis.
J. Caldas and S. Kaski. Journal of Computational Biology, 18(3):251-261, 2011

miRComp – Composite MicroRNA Target Prediction

miRComp

:: DESCRIPTION

miRComp is a filtering step of putative microRNA targets through aggregating the predictions by several algorithms using two composite statistics – composite ranks and composite “p-values”

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRComp

:: MORE INFORMATION

Citation

Jin Zhou, Shili Lin, Vince Melfi, Joe Verducci (2006).
Composite MicroRNA Target Predictions and Comparisons of Several Prediction Algorithms.
MBI Technical Report No. 51.

homoTarget – Prediction of microRNA targets in Homo Sapiens

homoTarget

:: DESCRIPTION

HomoTarget is a new algorithm for prediction of microRNA targets in Homo sapiens.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

HomoTarget

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 HomoTarget

:: MORE INFORMATION

Citation:

Genomics. 2012 Nov 19. pii: S0888-7543(12)00213-3. doi: 10.1016/j.ygeno.2012.11.005. [Epub ahead of print]
HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens.
Ahmadi H1, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A

BosFinder – pre-microRNA Gene prediction algorithm in Bos taurus

BosFinder

:: DESCRIPTION

BosFinder is a new algorithm which was developed to identify and annotate the whole genome’s derived pre-miRNAs.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

BosFinder

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BosFinder

:: MORE INFORMATION

Citation

Anim Genet. 2014 May 17. doi: 10.1111/age.12170. [Epub ahead of print]
BosFinder: a novell pre-microRNA gene prediction algorithm in Bos taurus.
Sadeghi B1, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A.

TarPmiR – microRNA Target Site Prediction

TarPmiR

:: DESCRIPTION

TarPmiR is a miRNA-mRNA binding sites prediction tool, which can utilize miRNA-mRNA binding experiment data such as CLASH (cross-linking ligation and sequencing of hybrids) .

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Python

:: DOWNLOAD

 TarPmiR

:: MORE INFORMATION

Citation:

TarPmiR: a new approach for microRNA target site prediction.
Ding J, Li X, Hu H.
Bioinformatics. 2016 May 20. pii: btw318.

WMD 3.2 – Web MicroRNA Designer

WMD 3.2

:: DESCRIPTION

WMD3 is a web app for the automated design of artificial microRNAs.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • Perl
  • gcc
  • MySQL
  • GenomeMapperBlast,
  • ViennaRNA

:: DOWNLOAD

 WMD

:: MORE INFORMATION

Citation

Plant Cell. 2006 May;18(5):1121-33. Epub 2006 Mar 10.
Highly specific gene silencing by artificial microRNAs in Arabidopsis.
Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D.

miRNAgFree – microRNA prediction using sRNAseq/miRNAseq/sncRNAseq

miRNAgFree

:: DESCRIPTION

miRNAgFree is a novel microRNA prediction approach based on biogenesis features, such as the known 5’ homogeneity, and duplex mean free energies which does not require a genome assembly.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VirtualBox.

:: DOWNLOAD

miRNAgFree

:: MORE INFORMATION

 

spongeScan – Detecting microRNA Binding Elements in lncRNA Sequences

spongeScan

:: DESCRIPTION

spongeScan is a web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.
Nucleic Acids Res. 2016 May 19. pii: gkw443.