Vbox appliance files (virtual machine archives) have been built and tested in Oracle's VirtualBox 5.x and 6.x under MS Windows 10 and MacOS 10.10 .. 11.5 host operating systems. The key advantage of this VM package is that all the non-trivial installation steps and dependencies on 64 bit and 32 bit libraries have been properly resolved. Note: We have recently noticed that older VBox versions (6.0.x, up to 6.1.2) are more stable than the latest releases. Under MacOS newer VBox versions experience a memory leak that blows the rquested amount of VM RAM)
VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold (Genetic Algorithm for RNA/DNA secondary structure prediction) installed. Note: no Galaxy/NanoTiler installed.
VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold (Genetic Algorithm for RNA/DNA secondary structure prediction) installed. Note: no Galaxy/NanoTiler installed.
VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, and StructureLab installed. Note: no Galaxy/NanoTiler installed.
VBox Virtual Machine appliance file (OVA) with RiboSketch, RNA_2D3D, StructureLab, and MPGAfold with Visualizer (Genetic Algorithm for RNA/DNA secondary structure prediction and GUI module) installed.
[Download (Mac)] | [Download (Windows 64 bit)] | [Download (Linux 64 bit)] | [Download (Processing Sketch)] |
RiboSketch is a drawing program for the production of single or multi-stranded RNA and DNA secondary structure images. Multiple strands (chains), non-canonical interactions, hybrid RNA-DNA base-pairing, pseudoknots, and interstrand interactions are supported. Circle diagams and other layout options are available, utilizing dynamic simulation mode (automatic "relaxed" layout) and/or fully interactive editing.
Installation: See the Ribosketch page for details.
[Download]
RNA2D3D (Linux binary, Open-GL GUI, links to Tinker for energy minimization) is an interactive software package for the conversion of 2D RNA to 3D structures. First pass conversion is based on purely geometric criteria (idealized A-form helices). Following it, the user can interactively refine the structure via such features such as H-loop shaping, helix compactification, designated helix stacking, and substitution of structure subsets with known 3D motifs (PDB). Energy minimization and short molecular dynamics runs relying on Tinker (automatically installed with kind permission of prof. J. Ponder) can be used for further refinements. Pseudoknots can be handled either automatically, or, if they are geometrically very complicated, built interactively by the user. RNA2D3D can also be used to build RNA-based nano structures, such as tecto-squares and meshes (see Chworos et al.,Science 306, 2004). The system comes with a directory containing several sample structures (including pseudoknots and tecto-square building blocks) and offers help information dealing with the big picture issues as well as usage details.
Installation:
Note: Revision 5.6.3. is newer and more stable than the previously designated rev. 5.7 (different development path).
Reference: Martinez, H., Maizel, J.V. Jr., and Shapiro, B.A. "RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA." J Biomol Struct Dyn. 2008 Jun;25(6):669-83.
[Download]
>NanoTiler is a Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).
Installation:
[Download] | [Online Version]
A software for predicting the concensus RNA secondary structure for a given alignment of nucleotide sequences.
Alternatively, try the KNetFold Web Server.
[Download]
The RSmatch package provides an approach to compare RNA structures, thereby uncovering functional structure elements. The software provides three different functions: 1) Pair-wise comparison and Database Search, 2) Multiple structure alignment with an extended mode to compute common structure, and 3) Iterative database search.
Note: The Vienna RNA package must be installed if sequences written in the FASTA format are used. The Vienna RNA package can be downloaded at www.tbi.univie.ac.at/~ivo/RNA/. For more information, please see datalab.njit.edu/biodata/rna/RSmatch/software.htm.
[Download]
[Download] | [Online Version]
The tar file contains souce files (C++) and 64-bit Linux binaries for the CorreLogo (same as our web server for the 3D sequence logos of RNA and DNA alignments).
Installation: Download, uncompress and extract the distribution files: tar -xfz correlogo_v1.2.6.tar.gz.
Alternatively, try the CorreLogo Web Server.
[Download]
The CovaRNA and CovStat software packages for detecting long-range covariations in nucleotide alignments. Reference: Bindewald and Shapiro: Computational deteaction of abundant nucleotide-covariation in Drosophila genomes. RNA, 2013.
Installation:
Contact: Wojciech (Voytek) K. Kasprzak, Wojciech.kasprzak@nih.gov