GeneCor

GeneCor

Applet link

What:
GeneCor illustrates some of the basic concepts behind gene sequencing. In the applet there is a series of 65 sequences, each consisting of 40 numbers in the range of approximately -3.3 to 3.3 . Each number is graphically shaded from white to dark purple. The user can select any two genes and compare the two both visually and through a correlation graph. The applet keeps track of the best and worst correlated pairs and can be tasked to search all 2080 combinations.

How:
Data canvas: The purple grid on the left consists of one large block of 65 rows, each row consisting of a white tab box on the far left, 40 data boxes of various purple shades across the middle and a white tab box on the far right. Two of the rows are highlighted with black outlines, one with the left tab filled black and one with the right tab filled black. These highlighted rows are duplicated for side-by-side comparison in two rows below the larger purple grid.
The user can select any two rows in the grid by clicking on one of the white tabs on the left or right side, highlighting that particular row. Note that a row can be selected for comparison against itself by selecting it on both the left and right.
Correlation graph: The numerical data for the sequences selected from the data canvas are plotted on the correlation graph, with the left-tab selected values on the horizontal axis and the right-tab selected values on the vertical axis. The applet calculates and graphs a least-squares linear fit and lists the computed correlation coefficient.
Optimal correlation lists: The applet tracks the correlation values for each selected pair of data, and retains the 5 highest (listed in green) and 5 lowest (listed in red) pair listings.
Run search button: Clicking this button will systematically search all pair combinations, ending with Gene 64 vs Gene 65. The best and ‘worst’ (most inverse) correlations for the entire data set will then be retained in the correlation lists.
Clear stack button: Clicking this button will erase the correlation lists.

Why:
This applet was a pilot example for a larger lesson on gene sequencing. The gene data numbers are real, however the context and specific interpretation of the data values is unavailable. A planned future version will visually illustrate the computer search process and improve upon the graphic interface.