GRAPHICS ONLINE

The presentation of graphics online presents a problem in that large graphic files load very slowly.  The following programs are designed to present data of a reasonable size.

Spinwave Graphics - (Spinwave, Wales) provides compression for GIF and JPG files.

Gif Tools - (GifTools.com) also provides compression for GIF and JPG files

  PDB2MultiGIF (Central Spectroscopy Department - Molecular Modeling, Deutsches Krebsforschungszentrum, Germany) which takes the 3D structure (PDB file) and generates an animated image which can be displayed using any browser. There is considerable choice on the image size, number of frames and direction of rotation. This is the bacteria transcription terminator factor rho.

For simple web-based plasmid drawing programs see   NetPlasmid (JustBio.com) or Savvy (Bioinformatics.org, Scalable Vector Graphics Plasmid Map; M.K. Basu).

For a very sophisticated online plasmid drawing program use   PlasMapper (Reference: X. Dong et al.2004. Nucleic Acids Res. 32 (Web Server issue):W660-4). This program will search for restriction sites, and in addition to permitting the user to diagram genes one can indicate the positions of promoters, terminators, replication origins with a large amount of control on picture properties and quality.  

red_bullet.gif (914 bytes) DNAPlotter - is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.(Reference: Carver, T. et al. 2008. Bioinformatics 25:119-120)

red_bullet.gif (914 bytes) GeneWiz (Center for Biological Sequence Analysis, Danish Technical University) produces linear or circular genome altases such as the one below.  They have ready name ones for most bacteria, but by uploading custom data in GenBank format (.gbk) one can make one's own diagram showing the genetic and physical properties of your genome.

red_bullet.gif (914 bytes) CGView Server - is a comparative genomics tool for circular genomes that allows sequence feature information to be visualized in the context of sequence analysis results. A genome sequence is supplied to the program in FASTA, GenBank, EMBL, or raw format. Up to three comparison sequences (or sequence sets) in FASTA format can also be submitted. The CGView Server uses BLAST to compare the genome sequence to the comparison sequences, and then converts the results and any available feature information (from the GenBank, EMBL, or optional GFF file) or analysis information (from an optional GFF file) into a high-quality graphical map showing the entire genome sequence, or a zoomed view of a region of interest. Several options are available for specifying how the BLAST comparisons are conducted, and for controlling how results are displayed. (Reference: Grant JR & Stothard P. 2008. Nucleic Acids Res. 36(Web Server issue):W181-184).  It also seems to be available here.

red_bullet.gif (914 bytes) 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, an example of which is given. 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)

red_bullet.gif (914 bytes) 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 onto the genome map.

red_bullet.gif (914 bytes) Gene Structure Display Server (GSDS2.0) is designed for the visualization of gene features, such as the composition and position of exons, introns, and conserved elements .etc. The input could be sequences, GenBank Accession Number (or GI), or features in BED/GTF/GFF3 formats. After inputting gene features, a high-quality image can be generated. Shape and color for features can be customized by users and further modifying functions on figures are provided. To facilitate evolutionary analysis, a phylogenetic tree can be uploaded and added on the figure. (Reference: B. Hu et al. 2015. Bioinformatics 31:1296-1297).

red_bullet.gif (914 bytes) CPGAVAS (Chinese Academy of Meduical Sciences) - Draw the Circular Map by providing a GFF3 or Tab-delimited file, which includes information on the colours used.

red_bullet.gif (914 bytes) FancyGene - is a fast and user-friendly web-based tool for producing images of one or more genes directly on the corresponding genomic locus. Starting from a variety of input formats, FancyGene rebuilds the basic components of a gene (UTRs, intron, exons). Once the initial representation is obtained, the user can superimpose additional features—such as protein domains and/or a variety of biological markers—in specific positions. (Reference: D. Rambaldi & F.D. Ciccarelli. 2009. Bioinformatics 25: 2281-2282)

red_bullet.gif (914 bytes) EZ Plasmid Map (J. Zhang, University of Texas, U.S.A.)

A number of resources are available to draw Venn diagrams:

  BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.  Good choice of colours. (Reference: T. Hulsen, et al. 2008. BMC Genomics 9: 488).
   Venny (Developed by Juan Carlos Oliveros, BioinfoGP, CNB-CSIC) - Basic graphical output with overlaps not to scale and basic colours.
 
 Venn Diagram Maker - lots of options
 Calculate and draw custom Venn diagrams
 
 Venn Diagram Plotter - Draws correctly proportioned and positioned two and three circle Venn diagrams whose colors can be customized and the diagrams copied to the clipboard or saved to disk.