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Analysis of Heteroduplex Mobility Shifts

This is a web executable version with a link to the full source release for HDent and HDdist, a pair of programs for analysing data from heteroduplex mobility and tracking assays (HMA and HTA). The HDent code can quantify the extent of variability in a lane and provide a linear correlation coefficient for variability over time. The HDdist code can quantify the level of difference between all lanes in a gel relative to a reference lane, and is useful for HTA or a situation where you might want to compare HMA signal in multiple lanes to a reference lane. Mark Muldoon wrote the code to provide portable, freely-distributable versions of the programs developed by D. Wolpert, B. Korber, A. Neumann, E. Delwart, and J. Mullins and employed in:

    E.L. Delwart, H. Pan, H.W. Sheppard, D. Wolpert, A.U. Neumann, 
    B. Korber & J.I. Mullins, "Slower Evolution of Human 
    Immunodeficiency Virus Type 1 Quasispecies during Progression 
    to AIDS", J. Virology, Vol. 71, pp.7498-7508, (1997).  Medline 
The form of this code is general, and could be applied to other gel based assays, or in fact to any data where signal was distributed through a series of bins, and one is interested in quantifying the entropy, or spread, of the signal.

The current release includes both Mac (CodeWarrior Pro 3.0) and Unix versions. To build the version for your platform, go to the appropriately named directory and follow the directions you find there. This website was created by Satish Pillai.

You can find the latest version of HD_tools on the web at http://www.ma.umist.ac.uk/mrm.

Use HDent for Heteroduplex Mobility Assays (HMA)

Use HDdist for Heteroduplex Tracking Assays (HTA)

last modified: Tue Oct 9 16:47 2007


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