HIV sequence database

**About HDdist:**

This is the front end for the command-line version of a program to calculate various measures of difference between the lanes in heteroduplex assays. Input should be in the same form as the HDdist sample input file. The program reads a file and stores all the scans of lanes that it finds there. Each scan should be recorded as a list of (pixel number, intensity) pairs. The program normalizes these lists so the total intensities are 1.0, then regards the results as probability distributions and computes various measures of the difference between them: 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). 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. Cosine dist. This measure is closely related to the L_2 distance: cos_dist = (L_2_dist^2)/ 2.0 The output lines will be of the form: year[[C]*] (n_pixels): [L1 diff] [L2 diff] [cosine diff] where the * indicates the sample that corresponds to the probe data and which distances get reported depends on the command line options. The default is to smooth with a kernel whose width is 1.5% the length of the scan and to report nothing; to see any output one *must* select at least one difference measure with the -d command line option. See HDdist sample output. **************************************************************** Acknowledgements: 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.

last modified: Tue Oct 9 16:41 2007