SoMART – Server for plant miRNA/tasiRNA Analysis Tools

SoMART

:: DESCRIPTION

SoMART (Solanaceae miRNA/tasiRNA Analysis Resources and Tools) is a web server for miRNA/tasiRNA analysis resources and tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs that potentially regulate genes of interest.

The server includes four sets of tools: ‘Slicer detector’ for detecting sRNAs targeting input genes, ‘dRNA mapper’ for detecting degradome (d)RNA products derived from input genes, ‘PreMIR detector’ for identifying miRNA precursors (MIRs) or tasiRNA precursor (TASs) of input sRNAs, and ‘sRNA mapper’ for mapping sRNAs onto input genes.

::DEVELOPER

Baker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Plant J. 2012 Jun;70(5):891-901. doi: 10.1111/j.1365-313X.2012.04922.x. Epub 2012 Mar 8.
SoMART: a web server for plant miRNA, tasiRNA and target gene analysis.
Li F1, Orban R, Baker B.

sRNAtoolbox 1.3.1 – Collection of small RNA Analysis tools

sRNAtoolbox 1.3.1

:: DESCRIPTION

sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools.The center piece of sRNAtoolbox is sRNAbench, which allows for expression profiling from deep sequencing experiments.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser / Linux

:: DOWNLOAD

sRNAtoolBox

:: MORE INFORMATION

Citation

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.
Aparicio-Puerta E, Lebrón R, Rueda A, Gómez-Martín C, Giannoukakos S, Jaspez D, Medina JM, Zubkovic A, Jurak I, Fromm B, Marchal JA, Oliver J, Hackenberg M.
Nucleic Acids Res. 2019 Jul 2;47(W1):W530-W535. doi: 10.1093/nar/gkz415.

Nucleic Acids Res. 2015 May 27. pii: gkv555.
sRNAtoolbox: an integrated collection of small RNA research tools.
Rueda A, Barturen G, Lebrón R, Gómez-Martín C, Alganza á, Oliver JL, Hackenberg M

RCAT 3.0 / CATUI 3.51 – RNA Comparative Analysis Tools

RCAT 3.0 / CATUI 3.51

:: DESCRIPTION

RCAT is a software infrastructure for the Comparative Analysis of RNA. The infrastructure consists of a novel database, RNA Comparative Analysis Database (rCAD) and an application for visualization/manipulation of data from rCAD, Comparative Analysis Toolkit User Interface (CATUI).

::DEVELOPER

the Gutell Lab

:: SCREENSHOTS

:: REQUIREMENTS

Microsoft Windows XP SP3, Vista, Windows 7 or Windows Server
.NET Framework 3.5, SP1 (rCAD Utilities) and .NET Framework 4.0 (CATUI)
rCAD: SQL Server 2008 Express Edition

:: DOWNLOAD

RCAT / CATUI

:: MORE INFORMATION

Citation

Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011)
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22.

Doshi K.J., Gardner D.P., Cannone.J.J, Gutell.R.R. and Smith M. (2010)
CATUI: The Comparative Analysis Toolkit User Interface
(manuscript in preparation)