RNAcop 1.0.3 – Optimizing RNA structures by Sequence Extensions

RNAcop 1.0.3

:: DESCRIPTION

RNAcop (RNA Context Optimization by Probability) is a tool for optimizing lengths of flanking regions up- and downstream of a constrained structure with respect to the probability of folding into the structure.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RNAcop

:: MORE INFORMATION

Citation

Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J.
Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. doi: 10.1093/nar/gkv813.

RNA2DMap v2 – Visual Exploration of RNA Structure

RNA2DMap v2

:: DESCRIPTION

RNA2DMap is a structural interface to comparative data. Currently, RNA2DMap presents three-dimensional RNA distances, tertiary interactions, conservation values, motifs, basepair groups, basepair conformations and coaxial stacks on interactive secondary structure models.

::DEVELOPER

the Gutell Lab

:: SCREENSHOTS

:: REQUIREMENTS

Adobe Flash Player

:: DOWNLOAD

RNA2DMap

:: MORE INFORMATION

Citation

Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011)
RNA2DMap: A Visual Exploration Tool of the Information in RNA’s Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA.

SARA 1.0.7 – Server for Function Annotation of RNA Structures

SARA 1.0.7

:: DESCRIPTION

SARA is a program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment. The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root-mean-square approach. The likely accuracy of the SARA alignments is assessed by three different P-values estimating the statistical significance of the sequence, secondary structure and tertiary structure identity scores, respectively.

::DEVELOPER

Structural Bioinformatics Unit

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Python
3dna

:: DOWNLOAD

SARA

:: MORE INFORMATION

Citation

Capriotti E, Marti-Renom MA. (2009).
SARA: a server for function annotation of RNA structures.
Nucleic Acids Research. 37 (Web Server issue): W260-W265.

GAISR – Genomic Analysis Illuminating RNA Structure

GAISR

:: DESCRIPTION

GAISR is a pipeline incorporating several de novo RNA discovery tools for finding, filtering and scoring ncRNA in operon and genome wide prokaryotes.

::DEVELOPER

the Meyer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX/Windows
Java

:: DOWNLOAD

GAISR

:: MORE INFORMATION

K2N – Service to Get from Knotted to Nested RNA Structures

K2N

:: DESCRIPTION

K2N (Knotted To Nested) a service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

K2N

:: 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.

SPuNC – RNA Structure Prediction using Nucleotide Composition

SPuNC

:: DESCRIPTION

SPuNC (Structure Prediction using Nucleotide Composition) provides a method for RNA structure prediction using evolutionary patterns of nucleotide composition.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SPuNC

:: MORE INFORMATION

Citation

Sandra Smit, Rob Knight, and Jaap Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition.
NAR (2009) 37(5):1378-86