HIV sequence database

HDdist

NOTE: Technical Support is not available for the program listed on this page.

HDdist calculates various measures of difference between the lanes in heteroduplex tracking assays (HTA). Click here for a more detailed explanation of this program and its applications.

Input

Upload your input file,
or paste your input here

Describe Your Gel

Enter a patient (if the gel represents a single patient) or gel ID
How many lanes are in your gel?	The reference lane, which should contain your probe and essentially be a homoduplex band, needs to be represented as the first lane, or first data set. If you ran it as a later lane in the gel, move the data up to the top of the file, as if it were the first lane.
How many pixels/positions has each lane been divided into by your gel scanner?
Enter a set of (space delimited) unique tags for each lane in your gel	You could just use lane numbers (1 2 3 4...), or if your lanes correspond to times, you could specify the time points (0 0.5 1.7 2.4 months from estimated time of infection, for example). If you use units of time for this, a subsequent option will allow you to calculate the correlation coefficient for variation over time.

Options

Report L_1 distance	This is the default measure of distance; it is the pixel-by-pixel sum of the absolute values of the differences in normalized intensity. This sum has a maximum value of 2.0, so we report (L_1 distance / 2.0) in order to get a result in the range (0.0, 1.0).
Report L_2 distance	Euclidean distance between the two distributions when each is regarded as a unit vector. It has a maximum value of sqrt(2.0). Here again we divide the distance by its maximum value in order to report a result between 0 and 1.
Report Cosine distance	This measure is closely related to the L_2 distance: cos_dist = (L_2_dist^2)/ 2.0
Calculate least-squares regression	Calculate the correlation coefficient of each of the reported measures against time, determined through least-squares regression. For this option to be meaningful, you should have entered units of time (above) to designate each lane in your gel.
Smooth the data	Smooth the data by convolving it with a Gaussian kernel having the specified width. The width should be specified as a fraction of the scan's length. The default is "-s 0.015"; that is, smoothing with a width of 1.5% of the scan's length (in pixels). A width of 0.0 forces the program to analyse the data raw, with no smoothing. Specify width:

Make sure that you have filled the form out correctly, then hit the Run button to begin remote processing.

last modified: Tue Oct 9 16:38 2007

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