BASIC PROTOCOL 7: USING THE GENOME BROWSER
All the sections of WormBase described so far consist mainly of written text. However, organisms have a text of their own, the genomic DNA sequence, within which important biological features reside. WormBase thus provides schematic diagrams of genomic DNA, as well as textual descriptions of genes, with a Generic Genome Browser that allows customizable views of C. elegans DNA (Stein et al., 2002).
A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)
Web browser such as Internet Explorer (http://www.microsoft.com) or Mozilla (http://www.mozilla.org/firefox)
1. Click the Genome link at the top left of the WormBase front page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png) to start the Genome Browser (http://wormbase.org/db/seq/gbrowse/wormbase/;
2. Select an appropriate search term. The Genome Browser requires a "Landmark or Region" (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_09.png), but this can include genome-wide scans for nucleotide sequences, gene classes, or key words in gene descriptions. Examples are given on the Genome Browser page. The Browser can view both linear nuclear chromosomes (autosomes 1 through 5, plus the sex chromosome X; (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_09.png), and the circular mitochondrial chromosome (MtDNA, shown as a line).
3. Click the Search button and examine the results. If a search term is used that has multiple hits in the genome (e.g., zyg-*), one will get a schematic view displaying their positions in the genome, with hypertext links.
Study a particular genomic region
4. Where there is more than one search result, click one link to see an individual genomic region
and decide which of its features to further examine.
Features of the given region are displayed by selecting specific bands or "tracks" for viewing the sequence from left to right. The view of a given region can be customized by many different "tracks." The default view is to have only a few tracks (e.g., gene models, GenBank entries, and operons), in order to make the initial view clear. However, the view can be expanded by adding more tracks (such as ESTs, restriction sites and alignments to C. briggsae) until it is quite elaborate. From a C. briggsae alignment, one can hop to the relevant segment of the C. briggsae genome. ESTs can be ordered from the research group of Yuji Kohara (firstname.lastname@example.org).
5. Select the most useful tracks, and click on the Update Image link.
The view will then show the added information tracks. One revised view is given in (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_10.png) In this case, alignments to C. briggsae, to "best" ESTs, and to "best" mRNAs have been invoked. Most ESTs in the region, and a single mRNA (identified by cDNA sequencing), support the structure of zyg-1. Two ESTs overlap the nested bli-2 gene, and bli-2-like sequences within zyg-1-like sequences are highly conserved in C. briggsae. Moreover, small regions of conserved sequence on the 5¬¢ flanks of the zyg-1 and bli-2 transcription units; these regions are reasonable candidates for transcriptional regulatory sequences (Nardone et al., 2004). Well-chosen tracks can thus show complex data in a compact, vivid way.
6. Optionally, adjust the scale of the genome view by clicking on the appropriate links in the Scroll/Zoom menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_09.png).
This is a small but powerful menu; it can expand the view to subchromosomal ranges of 1 Mb
or focus the view in to single-nucleotide resolution.
To get views of individual nucleotides, set the zoom for "100 bp" and switch on the track "DNA/GC Content." (At scales greater than 100 bp, this gives a graphical view of the percentage of GC nucleotides.) In either case, the location of the sequence shown within its entire chromosome is also diagrammed.
7. Another way to examine desired slices of the genome is to type in their exact coordinates into the "Landmark or Region" text field (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_09.png) and then click the Search button. Genomic coordinates are given in the format [chromosome]:[start nucleotide]..[final nucleotide]; for instance, the coordinates of zyg-1 are II:5649706..5654391. (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_04.png) By choosing coordinates and then adjusting them to improve the graphical view, it is possible to incrementally refine the region viewed to very high precision, starting with large changes and ending with small ones.
8. Given a particular region, one may want to extract its nucleotides for analysis. The Genome Browser enables this with the "Display Sequence File" option in the "Reports & Analysis" menu. When the viewer is set to the exact nucleotides wanted, select this option and then click the Go button to the right. This will produce a text file in FASTA format, which can then be saved to disk and manipulated with other programs such as EMBOSS (http://www.hgmp.mrc.ac.uk/Software/EMBOSS/).
9. If a particular object in the sequence view is itself worth examining, click on it to go to its record in the database. For instance, in the original view of zyg-1, one can click on the bli-2 gene and go to the Sequence page for bli-2/F59E12.12.
Normally, WormBase gives its views of the genome as ordinary bit-by-bit (raster-based) PNG diagrams in a Web browser. However, to publish a figure in a professional research journal, it is often preferable to have figures that are line drawings (scalable vector graphics, or SVG) instead of PNG diagrams. It is possible to generate publication-quality line drawings (SVG figures) from WormBase. Viewing these figures requires the SVG plugin for one's Web browser. See http://plugindoc.mozdev.org/linux.html for Mozilla/Linux plugins. Adobe SVG plugins for Macintosh and Windows systems are available at http://www.adobe.com/support/downloads/. SVG figures can then be further worked up for publication with a commercial program such as Adobe Illustrator, or open-source programs such as Inkscape (http://www.inkscape.org) or Batik (http://xml.apache.org/batik).
10. To get line drawings of a genomic region, click the "High-res Image" link in the Genome Browser menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_10.png). Follow the resulting instructions to save the newly generated SVG file to disk. To view the diagram immediately, one will need to have an appropriate SVG plugin for one's Web browser (see http://plugindoc.mozdev.org/linux.html for Mozilla/Linux plugins).
11. WormBase provides advanced functions to allow collaborative annotation of the genome by outside researchers. If it is desirable to provide annotations for a given region, open the "Add your own tracks" menu at the bottom of the Genome Viewer page, and then use the "Upload your own annotations" or "Add remote annotations" options. Help documents for these are available on-line.