Something!
This tool allows the user to annotate any data that can be displayed in three dimensions. It was
in particular designed to annotate metagenomic assemblies though clearly is not limited to this
use. To provide data for this site please contact the page administrator (in this case Doug Rusch).
The very first step is to select a data file to view. Once one has been selected a 3-D scatter
plot of the data will be displayed on the left. Each point represents a seperate data point. The
size of the point indicates the magnitude of the data (ie size of point correlates with the length
of the sequence). A set of controls allowing the user to rotate, translate, and otherwise
manimpulate the data are provided on the right. Below the controls are a list of pre-defined
categories. The name of the category, number of sequences in a category, the total length of those
sequences (in base pairs), and average length of each sequence (again in base pairs) is given.
There is also a drop down menu that allows the user to color or hide any particular category.
While the scatter plot can be manipulated with the control panel it can also be directly
manipulated using mouse movements while pressing certain keys:
shift-key rotate image along X or Y axis
control-key translate image in X or Y plane
alt-key while using mousewheel zooms in and out
One of the pre-defined categories includes a user specified group. Sequences can be added or
removed from this group by double-clicking on specific sequences in the scatter plot. Note that
when you double click only the top most (closest) sequence will be selected. If you mouse over
a given sequence the ID and length of the sequence will become visible after a short delay. When
a sequence is added to the user specified group the ID is added to a text area and the user
specified group is updated to reflect the addition of the new sequence. Sequences already in a
group can be added to a user specified group and will be colored accordingly. To remove a sequence
double click on the sequence again. When you have defined a group of interest you can copy the
sequences from the text area and use them as you deem necessary. Currently there is only a single
user specified group and there is no way to safe this information.
If you have any questions, comments, or bugs to report please contact:
Doug Rusch (drusch@jcvi.org).
Getting Started: Select a genome from the pull down menu to start.
