Fig 1.
Summary of the visualization method.
A source PNG image is generated to represent FASTA sequences. These source PNG images are then processed, including the creation of a Deep Zoom image pyramid. The resultant visualized interface includes scripts that compute nucleotide composition density and generate a GC skew graph.
Fig 2.
Screenshot of DNA Data Visualization generator (DDV) after it generates the source PNG for Frankia sp. CcI3 chromosome [GenBank: NC_007777].
User downloads/selects FASTA data file, selects the image height, and generates the source PNG image. The final step is to click on “Process Image with Deep Zoom” to complete the generation of a visualization interface for this dataset.
Fig 3.
Each nucleotide is 2px X 2px, with 70 nucleotides per line. The height (iHeight) is set to 3000 px for bacterial genomes, and the value can be increased for larger data sets. The total width (iWidth) depends on length of the data. Each visualization column is separated by 4px of grey padding.
Fig 4.
Screenshot of generated interface for visualized data set: Frankia sp. CcI3 genome [GenBank:NC_007777], 5433628 bp.
Screenshot taken after computing nucleotide density for the whole sequence, zooming in, generating GC-Skew plot for the sequence, and selecting a sequence fragment at bp 2882288. The interface includes a scale bar (bottom left of Deep Zoom viewer) shown in bp units, and a viewport navigator (top right of Deep Zoom viewer) that shows zoom position and can also be used for panning.
Fig 5.
DDV generator dependencies and visualized DNA Data interface files.
DDV is a C# application that generates sequence specific files for each DNA dataset, as well as the shared CSS, JavaScript, and PHP files in the output folder. The included civetweb serves the PHP files when the user is viewing the visualized interface on a local PC.
Fig 6.
Visualization of the major linear chromosome of Borrelia burgdorferi B31 [GenBank: NC_001318].
A) Whole linear chromosome of 910724 bp; B) enlargement of the segment surrounding the origin of replication (localized between coordinates 458036 and 458227). Arrows indicate the distance from the beginning of the chromosome sequence.
Fig 7.
Zoomed-in fragments of the visualization of the Streptomyces coelicolor A3(2) [GenBank: NC_003888] linear chromosome showing the rrnB and rrnA ribosomal gene clusters (coordinates 1916451 to 1921599 and 4530650 to 4535576). Arrows indicate the limits of each cluster. Empty arrows indicate the direction of chromosomal DNA replication fork movement and the direction of rRNA genes transcription.
Fig 8.
Visualization of the 16.5 kb-terminal segments of the Streptomyces davawensis JCM 4913 chromosome [GenBank: HE971709].
The segments are parts of the 33.3 kb LTIRs of this genome. A: image of the left end of the chromosome; B: 180°-rotated image of the right end of the chromosome.
Fig 9.
Visualization of the Clostridium difficile 630 chromosome [GenBank: NC_009089].
Segments corresponding to the seven known conjugative transposons are indicated by brackets. 1: CTn1; 2: CTn2; 3: CTn3, also known as Tn5397; 4: CTn 4; 5: CTn5; 6: CTn6; 7:CTn7.
Fig 10.
Comparison of the chromosomes of Clostridium difficile strains CD196 [GenBank: NC_013315] and R20291 [GenBank: NC_013316].
The region comprising transposons Tn6104, Tn6105 and Tn6106 is indicated by brackets. The two first corresponding RNA gene clusters are indicated by arrows for both strains.
Fig 11.
Examples of visualizations of tandem repeats in human chromosome 21 [GenBank: NC_000021.9].
The scale represents a segment of 20 nucleotides. A: microsatellite consisting of CA repeats (nucleotide coordinates 6565371–6566350); B: GGAAT tandem repeats, also known as DNA satellite III (7259491–7260680); C: imperfect [TCTA][TCTG] 4bp repeat in the D21S11 locus included in CODIS database (19181961–19182170). D: 171-base pairs repeat, also known as alphoid DNA satellite or α-satellite (7265231–7269080).
Table 1.
Source data files used to generate visualizations presented in Figs 4 and 6–11, along with URLs of the corresponding generated visualizations.