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HDent ReadMe

About HDent:

    This program performs Shannon entropy and median
mobility shift (MMS) calculations for heteroduplex
assays.  Input should be in the same form as the
HDent sample input file.

    The program reads the file and stores all the
scans it finds there.  Each scan is recorded as a list of 
(pixel number, intensity) pairs.  The program normalizes
this list so the total intensity is 1.0, then regards
the result as a probability distribution and computes
two statistics:

    median: the place in the lane which divides
            the scan's total signal in half.  If,
            for example, the lane has one broad band 
            in it, the median will fall somewhere in
            the middle of the band.

    entropy: a measure of the breadth of the distribution;
             this number is large for lanes with numerous
             smeared, overlapping bands and small for 
             lanes with a few small, tight bands.

    These statistics were first used to analyze data
from a heteroduplex mobility assay in a paper of
Delwart et al., J. Virology 71:7498-7508, 1997. Medline 

    The approach was developed to provide a
quantitative measure of the intrapatient genetic
diversification of HIV based on HMA and HTA 
experiments over the course of a single infection.
High rates of diversification were correlated with
long term survival.

***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).

    This program is the work of many people: Bette Korber,
David Wolpert, Avidan Neumann, Eric Delwart and Jim Mullins developed
the original version applied in Delwart et al.;  James Theiler 
wrote opt-3.5, the package used to handle command line
arguments and Mark Muldoon wrote the code you are reading.
This website was created by Satish Pillai.

Click here for a detailed explanation of program output.

last modified: Tue Oct 9 16:43 2007

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