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HDent

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

HDent performs Shannon entropy and median mobility shift (MMS) calculations for heteroduplex mobility assays (HMA). 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?
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 years 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
Click here for a more detailed explanation of program output
Flip the coordinate system used to report the median The median comes out as a position (0.0 <= median <= 1.0) where 0.0 refers to the bottom of the lane (nearest the homoduplex band) and 1.0 is the top. Selecting this option flips this convention so that 0.0 is the top of the gel and 1.0 is the bottom.
Calculate least-squares regression Calculate the correlation coefficient of each of the reported measures against time, determined through least-squares regression. To use this option, you must have entered units of time (above) to designate each lane in your gel.
Specify number of pixels to use in entropy calculation

IMPORTANT: When comparing results of different gel scans, make sure you specify the same number of pixels for each analysis (which must be less than or equal to the lowest resolution of all the scans).
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


Questions or comments? Contact us at seq-info@lanl.gov.

 
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