Ebbie-MM 4.3 – Analyze Single Mismatches of Small RNAs to the genome

Ebbie-MM 4.3

:: DESCRIPTION

Ebbie-MM (Ebbie-(mis)match) is a software that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications.

::DEVELOPER

H Alexander Ebhardt , Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Java
NCBI-Blast

:: DOWNLOAD

Ebbie-MM

:: MORE INFORMATION

Citation

H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bosta3 and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucl. Acids Res. (2009) 37 (8): 2461-2470

RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION

RNAFold – Create Batch files for the FOLD module of the GCG

RNAFold

:: DESCRIPTION

RNAFold is a freeware stand-alone program that creates batch files for the FOLD module of the GCG program package. RNAFold allows easy sliding-window analyses of RNA secondary structure by creating batch files with repeated calls to the FOLD module. This program does not calculate RNA folding energies directly.

::DEVELOPER

Lawrence’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

RNAFold

:: MORE INFORMATION

MicroTar 0.9.6 – microRNA Target Prediction from RNA Duplexes

MicroTar 0.9.6

:: DESCRIPTION

MicroTar is a microRNA target prediction program based on mRNA sequence complementarity (3′-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA molecules. It uses the RNAlib library from the Vienna RNA package.

::DEVELOPER

Tammi Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux

:: DOWNLOAD

MicroTar Serial version ; Parallel (MPI) version

:: MORE INFORMATION

Citation:

Thadani R, Tammi MT (2006).
MicroTar: predicting microRNA targets from RNA duplexes
BMC Bioinformatics 7:S20.

Knotted2Nested – Remove Pseudoknots from RNA

Knotted2Nested

:: DESCRIPTION

Knotted2Nested removes pseudoknots from a list of RNA base pairs, using different algorithms. It produces in pseudoknot-free (dot-bracket) 2D structures.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

Knotted2Nested

:: MORE INFORMATION

Citation

Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight.
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA (2008) 14(3):410-416.