Tag: Study

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

GENBMAP 1.0 – Study of the Spatial Genetic Structure

GENBMAP 1.0

:: DESCRIPTION

GENBMAP (Genetical Bandwith Mapping) is a software for the study of the spatial genetic structure. It was developped by Alain Cercueil, O. Fran?ois and S. Manel. The method is essentially descriptive, and allows an user to analyze genotypes and geographic coordinates simultaneously through a two dimensional graphical representation. GenBMAP provides a basis for the interpretation of the genetic structure of a population.

::DEVELOPER

the Computational and Mathematical Biology group in Grenoble

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GENBMAP

:: MORE INFORMATION

Citation

Cercueil A, François O, Pidancier N, Manel S
The Genetical Bandwidth Mapping: A spatial and graphical representation of population genetic structure based on the Wombling method
Theoretical Population Biology Volume 71, Issue 3, May 2007, Pages 332–341

ANACONDA 2.0 – Study of Genes’ Primary Structure

ANACONDA 2.0

:: DESCRIPTION

ANACONDA is a software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

::REQUIREMENTS

  • Windows

:: DOWNLOAD

  ANACONDA

:: MORE INFORMATION

Citation

Methods Inf Med. 2006;45(2):163-8.
Statistical, computational and visualization methodologies to unveil gene primary structure features.
Pinheiro M, Afreixo V, Moura G, Freitas A, Santos MA, Oliveira JL.

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