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

RocketBugs / RocketBugsRender – Simulation of the Actin-based Motility of Listeria Monocytogenes

RocketBugs / RocketBugsRender

:: DESCRIPTION

RocketBugs is a simulation of the actin-based motility of Listeria monocytogenes.

RocketBugsRender is a special rendering and graphing program for the simulation output of “RocketBugs”, the actin-based Listeria motility simulations

::DEVELOPER

The Center for Cell Dynamics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

RocketBugs  ,RocketBugsRender

:: MORE INFORMATION

Citation

Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell
An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
PLoS Comput Biol 5(7): e1000434. doi:10.1371/journal.pcbi.1000434

ParMSpindle 1.0 – Simulation of the ParM mediated Segregation of Bacterial Plasmids

ParMSpindle 1.0

:: DESCRIPTION

ParMSpindle is a 3D, force-based simulation of the ParM mediated segregation of bacterial plasmids, tracking the biochemical state of each monomer with experimentally determined filament dynamics

::DEVELOPER

The Center for Cell Dynamics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

   ParMSpindle

:: MORE INFORMATION

BATMAN-TCM – Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

BATMAN-TCM

:: DESCRIPTION

BATMAN-TCM is an online bioinformatics analysis tool specially designed for the research of molecular mechanism of TCM.

::DEVELOPER

BATMAN-TCM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F.
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine.
Sci Rep. 2016 Feb 16;6:21146. doi: 10.1038/srep21146. PMID: 26879404; PMCID: PMC4754750.

SimPlot 3.5.1 – Sequence Similarity Plotting

SimPlot 3.5.1

:: DESCRIPTION

SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimPlot if you cannot make that work, please email me for a download link

:: MORE INFORMATION

Reference to the paper in which author first described SimPlot

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.

VisSPA 1.62 – Calculate Frequency of Residues

VisSPA 1.62

:: DESCRIPTION

VisSPA (Visual Signature Pattern Analysis) is a program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were initially inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VisSPA

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

VarPlot 1.2 – Similarity Plotting for Alignment of Sequences

VarPlot 1.2

:: DESCRIPTION

VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VarPlot

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

MargFreq 1.02 – Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence

MargFreq 1.02

:: DESCRIPTION

MargFreq is a relatively user-friendly Windows program that does a repetitive task – calculating the marginal frequencies at each position of a nucleotide/amino acid sequence. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MargFreq

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

CleanCollapse 1.0.5 – Transfer Alignment of Sequences into Single Sequence

CleanCollapse 1.0.5

:: DESCRIPTION

CleanCollapse is a relatively user-friendly Windows program that accepts an alignment of sequences, and optionally can remove rare sporadic polymorphisms that may represent analytical artifacts, and also reduce redundancy by “collapsing” identical sequences into a single sequence. The program provides a record of these manipulation, and some rudimentary analysis (e.g. proportion of synonymous and nonsynonymous sporadic changes) that may assist interpretation

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CleanCollapse

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data

NimbleTree 2.6

:: DESCRIPTION

NimbleTree is a relatively user-friendly Windows program for making phylogenetic trees starting from sequence data.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NimbleTree

:: MORE INFORMATION

Before you download software you need to read disclaimer.

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