Genome Visualization
Proksee
Proksee (Paul Stothard, Univ. Alberta, Canada) - is an updated version of my go-to program for analysis and visualization of bacterial and phage genomes - CGView Server. This version includes integrated genome annotation tools and a new CGView engine written in JavaScript that allows for rapid zooming to the DNA sequence level. Extensive options are available for customizing maps and highlighting features of interest. (Instructions)
PlasMapper 3.0
PlasMapper 3.0
- allows users to generate, edit, annotate and interactively visualize
publication quality plasmid maps. Additionally, it offers an option of
automated codon optimization and BLAST sequence alignment.
(Reference: Wishart DS et al. 2023. Nucleic Acids
Res 51(W1): W459-W467).
JPGV
Jena Prokaryotic Genome Viewer (JPGV) - from a GenBank flatfile (*.gbk) generates linear or circular plots; including if desired GC content, GC skew, purine excess and keto excess can be displayed. Also allows BLAST analysis against related genomes. Requires free registration.
GenomeVx
GenomeVx
- makes editable, publication-quality, maps of mitochondrial and
chloroplast genomes and of large plasmids. These maps show the location
of genes and chromosomal features as well as a position scale. The
program takes as input either raw feature positions or GenBank records.
In the latter case, features are automatically extracted and colored.
Output is in the Adobe Portable Document Format (PDF) and can be edited
by programs such as Adobe Illustrator.
(Reference: G. Conant & K. Woolfe. 2008.
Bioinformatics 24:861-862).
myGenomeBrowser
myGenomeBrowser
- is a web-based environment that provides biologists with a way to
build, query and share their genome browsers. This tool, that builds on
JBrowse, is designed to give users more autonomy while simplifying and
minimizing intervention from system administrators. They have extended
genome browser basic features to allow users to query, analyze and share
their data.
(Reference: S. Carrere & J. Gouzy. Bioinformatics
(2017) 33 (8): 1255-1257).
OrganellarGenomeDRAW
OrganellarGenomeDRAW
- is a suite of software tools that enable users to create high-quality
visualrepresentations of both circular and linear annotated genome
sequences provided as GenBank files oraccession numbers. Although all
types of DNA sequences are accepted as input, the software has
beenspecifically optimized to properly depict features of organellar
genomes. A recent extension facilitates theplotting of quantitative gene
expression data, such as transcript or protein abundance data, directly
ontothe genome map
(Reference:Lohse M, et al. 2013. Nucleic Acids Res.
41(Web Server issue):W575-81).
PlasmaDNA
PlasmaDNA
- Starting with a primary DNA sequence, PlasmaDNA looks for restriction
sites, open reading frames, primer annealing sequences, and various
common domains. The databases are easily expandable by the user to fit
his most common cloning needs. PlasmaDNA can manage and graphically
represent multiple sequences at the same time, and keeps in memory the
overhangs at the end of the sequences if any. This means that it is
possible to virtually digest fragments, to add the digestion products to
the project, and to ligate together fragments with compatible ends to
generate the new sequences. Excellent package for plasmids.
(Reference: Angers-Loustau A et al. 2007. BMC Mol
Biol. 2007; 8:77).
GECA
GECA
- is a user-friendly tool for representing gene exon/intron organization
and highlighting changes in gene structure among members of a gene
family. It relies on protein alignment, completed with the identification
of common introns in the corresponding genes using CIWOG. GECA produces a
main graphical representation showing the resulting aligned set of gene
structures, where exons are to scale. The important and original feature
of GECA is that it combines these gene structures with a symbolic display
highlighting sequence similarity between subsequent genes. It is worth
noting that this combination of gene structure with the indications of
similarities between related genes allows rapid identification of possible
events of gain or loss of introns, or points to erroneous structural
annotations. The output image is generated in a portable network graphics
format which can be used for scientific publications.
(Reference: Fawal N, et al. 2012. Bioinformatics;
28:1398-9).
Updated: December, 2025