GenomeVx Help
GenomeVx is a tool for generating PDF diagrams of circular chromosomes. The output it produces is suitable for editing in programs such as Adobe Illustrator.
The input to GenomeVx is a series of genes with starting and ending coordinates. A strand identifier is also required for each gene. Genes can be optionally colored using a color field.
GenomeVx also has the ability to read GenBank chromosome description files and to upload the chromosome features from this source. At present, only protein-coding genes, tRNAs and rRNAs are upload. An optional auto-coloring feature is available.
Field Specific Help
Citation
Conant, G. C., and K. H. Wolfe. (2007) GenomeVx: Simple web-based creation of editable circular chromosome maps, Bioinformatics, in press.
Source code requests
The c code for GenomeVx is somewhat technical to use, but we are happy to distribute it on request:
conantg@tcd.ie.
Known Issues
Bug fixes
- 7/7/08: Updated the handling of GenBank files to correctly read more gene names from rRNA and tRNA genes
- 7/7/08: Changed input handling to allow plotting of larger genomes
- 10/01/08: Fixed a problem where mismatched empty lines in the misc. features columns would give errors
- 10/01/08: Adjusted how the scale ticks are calculated
- 10/02/08: GenomeVx will now read Genbank files where features are CDS tagged instead of gene tagged
- 12/09/09: Fixed a problem where mismatched empty lines in the Starts, Ends and Colors columns would give errors. (See 10/01/08 bug fixes)
- 8/16/10: Fixed a bug whereby GenomeVx would fail to draw a map if colors were not specified in the main gene list but misc. features were entered.
- 4/10/12: Fixed a bug whereby GenomeVx would fail to detect a missing strand code when the null string was given as a strand code
- 7/6/12: Migrated GenomeVx to new hardware, updated contact information for G. Conant
- 2/28/13: Added the option to allow autocoloring of user input data
- 7/26/16: Fixed a bug causing the drawing of too many internal rings