• The phylotree and multiple sequence alignment component associated with the gene families have been upgraded to provide significantly more control over coordinated display of subsets of genes of interest, which we hope will help users tailor the displays for the specific questions they are asking, especially with respect to very large gene families and as the number of species included in the families continues to grow. For example, by interacting with the list of species displayed in the legend, one can choose to restrict the tree and alignment to show only members from a subset of species; similarly, the clicking on internal nodes of the trees now provides options to focus in on the subtree rooted at that node, or to collapse and hide the subtree at the node. Other sorts of inter-component interactions are also provided, such as the ability to select sequences from the alignment and see the corresponding nodes in the tree highlighted. You can try these new features out now on this family and click on the Gene Family Help to get access to an interactive tour.
  • The LIS InterMines for soybean, common bean and peanut have been updated with several new features, including
    • Genetic map displays
    • Expression heat maps now available directly from gene lists.
    • Explicit representation of up/downstream flanking regions of genes and introns, with associated list-based analyses for shared motifs

    If you have thoughts on other analyses of this sort that would be useful for us to incorporate, feel free to contact us and give suggestions.