{version = 1.05; (* of chaos.p 1996 October 21} (* begin module describe.chaos *) (* name chaos: chaotic analysis of scan data synopsis chaos(data: in, xyin: out, output: out) files data: data from the scan program xyin: data rearranged for chaotic analysis plot. The file format is ready for input to xyplo. output: messages to the user description A "classical" test for chaos in a system is to transform the series: x1, x2, x3, x4, x5, ... Into a set of pairs of coordinates: (x1,x2) (x2,x3) (x3,x4) (x4,x5) ... If there is no relationship, then one gets a random-looking scatter diagram. If there is a chaotic relationship, one gets curves. This program uses the potential locations of binding sites found by the scan program (and output in file 'data') as the input series. These values are then weighted by their probability. examples data: * DEFINITION OF THE DATA COLUMNS: * 1 piece number * 2 piece length * 3 piece name * 4 piece coordinate * 5 matrix orientation (+1 = as in book, -1 = complement) * 6 Ri evaluation (bits per site) * 7 Z * 8 probability * 1 87192 p1 15 1 2.184500 -2.223394 0.013095 1 87192 p1 81 1 1.000218 -2.648260 0.004045 1 87192 p1 88 1 2.780186 -2.009690 0.022232 1 87192 p1 109 1 5.395104 -1.071578 0.141955 1 87192 p1 113 1 1.761704 -2.375074 0.008773 1 87192 p1 165 1 1.217743 -2.570222 0.005082 1 87192 p1 387 1 3.648239 -1.698272 0.044728 1 87192 p1 447 1 1.022737 -2.640181 0.004143 1 87192 p1 480 1 2.553458 -2.091029 0.018263 1 87192 p1 528 1 6.956904 -0.511276 0.304579 1 87192 p1 540 1 2.927385 -1.956881 0.025181 1 87192 p1 587 1 1.316462 -2.534806 0.005625 1 87192 p1 609 1 6.937751 -0.518147 0.302178 1 87192 p1 621 1 1.241720 -2.561620 0.005209 1 87192 p1 625 1 2.097234 -2.254701 0.012076 1 87192 p1 705 1 1.965286 -2.302038 0.010667 1 87192 p1 992 1 3.166391 -1.871137 0.030663 1 87192 p1 1108 1 1.757896 -2.376440 0.008740 documentation see also scan.p, xyplo.p author Thomas Dana Schneider bugs The program uses the coordinates reported in the data file. Since these are piece coordinates they are not necessarily linear (ie, 1 to n). If fragments have been extracted from a circular sequence, the results will have some incorrect data. (This is a minor bug.) technical notes *) (* end module describe.chaos *) {This manual page was created by makman 1.44}{created by htmlink 1.55}