Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

SARSE 1.37 – RNA Sequence Editor

SARSE 1.37

:: DESCRIPTION

SARSE (semiautomated RNA sequence editor) is a graphical sequence editor for working with structural alignments of RNA.

::DEVELOPER

E. S. Andersen, A. Lind-Thomsen and J. Gorodkin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SARSE

:: MORE INFORMATION

Citation:

Semiautomated improvement of RNA alignments
E. S. Andersen, A. Lind-Thomsen, B. Knudsen, S. E. Kristensen, J. H. Havgaard, E. Torarinsson, N. Larsen, C. Zwieb, P. Sestoft, J. Kjems and J. Gorodkin,
RNA 13:1850-1859, 2007.

ddbRNA – RNA Secondary Structure Prediction

ddbRNA

:: DESCRIPTION

ddbRNA is a software for detection of conserved secondary structures in multiple alignments.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ddbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Sep 1;19(13):1606-11.
ddbRNA: detection of conserved secondary structures in multiple alignments.
di Bernardo D, Down T, Hubbard T.

SEECER 0.1.3 – SEquencing Error CorrEction for Rna reads

SEECER 0.1.3

:: DESCRIPTION

SEECER is an error correction method that removes errors that are introduced during sequencing. Mismatches, insertion or deletions are removed by creating multiple alignments of reads and building HMMs that are used to decide which reads are be corrected. In the provided reference it is shown that error correction with SEECER improves the downstream analysis, especially RNA de novo assembly.

::DEVELOPER

Hai-Son Le , Marcel Schulz , Ziv Bar-Joseph

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SEECER

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215
Probabilistic error correction for RNA sequencing.
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.

NOFOLD 1.0.1 – RNA Structure Clustering without Folding or Alignment

NOFOLD 1.0.1

:: DESCRIPTION

NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

NOFOLD

:: MORE INFORMATION

Citation

Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.

VERSE v1.0.5 – Versatile and Efficient RNA-Seq Read Counting Tool

VERSE v1.0.5

:: DESCRIPTION

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

VERSE 

:: MORE INFORMATION

Citation

Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint).
VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

RNA Self Containment – Calculates the Self-Containment Index

RNA Self Containment

:: DESCRIPTION

The RNA Self Containment calculates the Self-Containment Index (SC). It measures the robustness of RNA substructures to changes in their surrounding sequence context, which we hypothesize to be a hallmark of structural modularity.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

 RNA Self Containment

:: MORE INFORMATION

Citation

M.T. Lee and J. Kim. 2008.
Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs.”
PLoS Comp. Biol., 4(8):e1000150 doi:10.1371/journal.pcbi.1000150.

RNASim 1.0 – RNA Evolution Model

RNASim 1.0

:: DESCRIPTION

RNASim is an implementation of the RNA evolution model. It simulates RNA evolution on phylogenies.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  RNASim

:: MORE INFORMATION

Citation

Large-Scale Simulation of RNA Macroevolution by an Energy-Dependent Fitness Model.
Sheng Guo, Li-San Wang, Junhyong Kim  2009
arXiv:0912.2326 [q-bio.PE]

siDirect 2.0 – Target Specific siRNA online Design Site

siDirect 2.0

:: DESCRIPTION

siDirect is a web server for providing efficient and target-specific siRNA design for mammalian RNAi. In this new version, the siRNA design algorithm has been extensively updated to eliminate off-target silencing effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability of the ‘seed’ duplex.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.
Naito Y, Yoshimura J, Morishita S, Ui-Tei K.
BMC Bioinformatics. 2009 Nov 30;10:392. doi: 10.1186/1471-2105-10-392.

ParaRNA 1.0 – Computing Parametric Alignment of Two RNA Structures

ParaRNA 1.0

:: DESCRIPTION

ParaRNAis a software for computing parametric alignment of two RNA structures. It takes two RNA secondary structures and match score, indel score, the range of mismatch score and the range of gap score as its input, and computes all the optimal alignments in the parametric space given by mismatch score and gap score, and show them in a graphic interface.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ParaRNA

:: MORE INFORMATION