RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION

GenomePixelizer 2003.10.1 – Genome Visualization Tool

GenomePixelizer 2003.10.1

:: DESCRIPTION

GenomePixelizer is a visualization tool that generates custom images of the physical or genetic positions of specified sets of genes in whole genomes or parts of genomes. Multiple sets of genes can be shown simultaneously with user-defined characteristics displayed. It allows the analysis of duplication events within and between species based on sequence similarities. GenomePixelizer may be useful in the detection of duplication events in genomes, tracking the “footprints” of evolution, as well as displaying the genetic maps and other aspects of comparative genetics.

GenomePixelizer may be considered a drawing tool that generates custom images of genomes out of the given set of genes. Each element on the picture has a physical address defined by coordinates (pixels), hence the name “GenomePixelizer”.

::DEVELOPER

GenomePixelizer Team, University of California

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Tcl/Tk

:: DOWNLOAD

GenomePixelizer

:: MORE INFORMATION

Citation

A. Kozik, E. Kochetkova and R. Michelmore
GenomePixelizer—a visualization program for comparative genomics within and between species
Bioinformatics (2002) 18 (2): 335-336.

DNPTrapper 1.0 – Assembly Editing & Visualization Tool

DNPTrapper 1.0

:: DESCRIPTION

DNPTrapper, a shotgun sequence finishing tool, designed to address the key sequence assembly problems caused by repeated regions in a genome. The program detects and visualizes single nucleotide differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.

::DEVELOPER

Tammi Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

DNPTrapper

:: MORE INFORMATION

Citation:

BMC Bioinformatics, 2006 Mar 20; 7:155
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
Arner, E, Tammi, MT, Tran, AN, Kindlund, E, Andersson B.