Top Tips

Top tip:

Vizualising gene trees. Did you know that you could visualize the Gene Tree between a gene and its homologs? It is reachable from the left-hand tab of the geneview pages, under ‘gene tree info.’ The Gene Trees represent the evolutionary history of gene families. Red squares represent duplications nodes, blue squares represent speciation nodes. Clicking on an internal node gives a pop-up-menu with indications on its taxonomy and clicking on a gene gives its gene and protein IDs (linking to the cognate page), and various information. The green bars at the right of the tree are a schematic representation of the multiple alignment of the peptides made using MUSCLE. Full boxes indicate matches/mismatches, open boxes indicate gaps in the alignment.

Updated on February 2014: It is reachable from the left-hand menu of the ‘Gene’ pages, under ‘gene tree (image).’

Top tip:

Selecting regions Did you know you could use the mouse to draw a rectangular region on the genome browser windows and then zoom into that exact region. This is very useful when you want to focus on a particular feature (gene, exon, microarray probe, etc). It works in all the graphical display panels of ContigView.

Updated on February 2014: If you go to the "Location Tab", in the Genome Browser, the "Region in Detail"(middle panel) will have a new icon called "switch to scrollable image". If you click on this icon three new features are available:

  • Scroll: navigate up or down in the chromosome or supercontig 5 Mb a the time. To update the bottom panel click on "update this image" or "Reset scrollable image".
  • Track height: certain tracks can be set to a fixed height of your choice, or to automatically expand or contract to fit all the features on the page.
  • Drag/Select: Using the mouse "Drag" or "Select" a region.