Tag: CGView

CCT – CGView Comparison Tool

CCT

:: DESCRIPTION

CCT is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized.

::DEVELOPER

Paul Stothard

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CCT

:: MORE INFORMATION

Citation:

Grant JR, Arantes AS, Stothard P (2012)
Comparing thousands of circular genomes using the CGView Comparison Tool.
BMC Genomics 13:202.

CGView 1.0 – Generat Maps of Circular Genomes

CGView 1.0

:: DESCRIPTION

CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes.Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

::DEVELOPER

Paul Stothard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

CGView

:: MORE INFORMATION

Citation:

Stothard P, Wishart DS.
Circular genome visualization and exploration using CGView.
Bioinformatics 21:537-539.