TransTreeView Help

TransTreeView is a unique tool which give a user the power to view the conservation profile of a binding site across the bacterial phylogenetic tree. The user will choose a pre-computed position weight matrix as well as a set of genes they wish to study. Orthologs of those genes are obtained from all genomes, and the upstream sequences are then searched for pre-computed hits to the PWM. If a hit is present, the tree node is highlighted.

TransTreeView Options

Help for TransTreeView options
  • A - Select a binding site profile from this list. You may view the details of this profile by clicking on the "Show Information" button while a profile is highlighted.
  • B - Once a profile is selected, click on the "Add to Query" button and your profile will be displayed in the "Profile Options" table. You may add many profiles if you wish to view more then one profile side by side.
  • C - Use this section to add a particular gene to your query.
    • Select a genome from the drop down list.
      (Optionally, You may filter the drop down list by typing in a few letters of the genome you are searching for.)
    • Then type in the name of the gene you are searching for.
      (You may use any of the names used in the Genbank RefSeq annotations.)
    • Then click on "Add to Query" to add this gene to the "Gene Options" selection.
      (If the gene was not found, you will be notified of this. You may add many genes if you wish to study a number of genes in a single query.)
  • D - If the consider operons option is selected, genes which are in the putative operon are also searched.
    (an operon is defined as a set of genes in the same direction with each gene less then 50bp apart)
  • E - Click on "Update Tree" to submit you query to the RegTransBase server.
    (Results can take from less then a minute to many minutes depending on the complexity of the query and server load.)

TransTreeView Results

Help for TransTreeView results
  • A - A taxonomic tree of bacterial genomes. The color of each row is explained below.
  • B - The number of genes orthologus to the query genes entered by the user. You may hover over the number to view the name of the gene.
  • C - The number of putitive binding sites found upstream of genes orthologus to the query genes entered by the user. You may hover over this number to see the name of the binding site, the distance to the gene, and other information.
  • a - Rows colored blue are genomes which contain an ortholog to the query gene as well as at least one putitive binding site upstream of the gene.
  • b - Rows colored light blue are genomes which contains a putitive binding site upstream of a gene in the same operon as the query gene.
  • c - Rows colored orange contain an ortholog of the query gene, though no binding site is found in its upstream sequence.
  • d - Rows colored black contain no ortholog of the query gene.