Tag: miRNA

mirnaTA 1.2.3 – miRNA Temporal Analyzer

mirnaTA 1.2.3

:: DESCRIPTION

mirnaTA is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies.

::DEVELOPER

mirnaTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 mirnaTA

:: MORE INFORMATION

Citation:

miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation.
Cer RZ, Herrera-Galeano JE, Anderson JJ, Bishop-Lilly KA, Mokashi VP.
Gigascience. 2014 Oct 13;3:20. doi: 10.1186/2047-217X-3-20.

miRClassify 1.0 – miRNA Family Classification and Annotation

miRClassify 1.0

:: DESCRIPTION

miRClassify is a novel machine learning-based web server which can rapidly identify miRNA from the primary sequence and classify it into a miRNA family in regardless of similarity in sequence and structure.

::DEVELOPER

Data Mining Group, Xiamen University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA
  • Apache-Tomcat

:: DOWNLOAD

 miRClassify

:: MORE INFORMATION

Citation

Quan Zou*, Yaozong Mao, Lingling Hu, Yunfeng Wu, Zhiliang Ji*.
miRClassify: An advanced web server for miRNA family classification and annotation.
Computers in Biology and Medicine. 2014, 45:157-160.

miREE – miRNA Recognition Elements Ensemble

miREE

:: DESCRIPTION

miREE is a novel microRNA target prediction tool consisting of two parts entailing complementary but integrated roles in the prediction.

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miREE: miRNA recognition elements ensemble.
Reyes-Herrera PH, Ficarra E, Acquaviva A, Macii E.
BMC Bioinformatics. 2011 Nov 24;12:454. doi: 10.1186/1471-2105-12-454.

MirtronPred – Intronic miRNAs Predictor

MirtronPred

:: DESCRIPTION

MirtronPred is a web based server to predict mirtrons from intronic sequences.

::DEVELOPER

Bioinformatics Centre ICGEB New Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genomics. 2012 Jun;99(6):370-5. doi: 10.1016/j.ygeno.2012.04.002. Epub 2012 Apr 21.
Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons.
Joshi PK1, Gupta D, Nandal UK, Khan Y, Mukherjee SK, Sanan-Mishra N.

TFmiR 1.2 – Disease-specific miRNA/Transcription Factor Co-regulatory Networks

TFmiR 1.2

:: DESCRIPTION

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis.

::DEVELOPER

Mohamed Hamed, Christian Spaniol, Maryam Nazarieh, & Volkhard Helms, Chair of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.
Hamed M, Spaniol C, Nazarieh M, Helms V.
Nucleic Acids Res. 2015 May 5. pii: gkv418.

C-mii 1.11 – Computational miRNA Identification

C-mii 1.11

:: DESCRIPTION

C-mii is specially designed and developed for identifying plant microRNAs and their targets.

::DEVELOPER

Information Systems Laboratory at BIOTEC

:: SCREENSHOTS

C-mii

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 C-mii

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 7:S16. doi: 10.1186/1471-2164-13-S7-S16. Epub 2012 Dec 13.
C-mii: a tool for plant miRNA and target identification.
Numnark S1, Mhuantong W, Ingsriswang S, Wichadakul D.

miRtest 1.8 – Combined miRNA- and mRNA-testing

miRtest 1.8

:: DESCRIPTION

Expression levels of mRNAs are among other factors regulated by microRNAs. A particular microRNA can bind specifically to several target mRNAs and lead to their degradation. Expression levels of both, mRNAs and microRNAs, can be obtained by microarray experiments. In order to increase the power of detecting microRNAs that are differentially expressed between two different groups of samples, “miRtest” incorporates expression levels of their related target gene sets.

::DEVELOPER

miRtest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 miRtest

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38365. doi: 10.1371/journal.pone.0038365. Epub 2012 Jun 19.
Detection of simultaneous group effects in microRNA expression and related target gene sets.
Artmann S1, Jung K, Bleckmann A, Beissbarth T.

miRPD – miRNA Protein Disease Associations

miRPD

:: DESCRIPTION

miRPD is a web server in which miRNA-Protein-Disease associations are explicitly inferred.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH), JensenLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 miRPD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 1;30(3):392-7. doi: 10.1093/bioinformatics/btt677. Epub 2013 Nov 21.
Protein-driven inference of miRNA-disease associations.
Mørk S1, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen LJ.

miRMOD 0.4 – miRNA Modification Identification tool

miRMOD 0.4

:: DESCRIPTION

miRMOD is the first windows based standalone GUI tool to identify and analyze non templated nucleotide additions and trimming at both the termini of the miRNA sequences in NGS data.

::DEVELOPER

Bioinformatics Centre ICGEB New Delhi

:: SCREENSHOTS

miRMOD

:: REQUIREMENTS

:: DOWNLOAD

 miRMOD

:: MORE INFORMATION

Citation

miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data.
Kaushik A, Saraf S, Mukherjee SK, Gupta D.
PeerJ. 2015 Oct 20;3:e1332.