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{version = 1.16; (* of winrs.p 1996 April 10} (* begin module describe.winrs *) (* name winrs: Compute Rs/window vs window in a single program synopsis winrs(book: in, cmp: in, winrsp: in, xyin: out, output: out) files book: A book from Delila. Only the first DNA piece in the book is used. cmp: A composition from the comp program. If cmp is empty, then equal frequencies are assumed. winrsp: : Parameters to control the program: one per line StartCoordinate (integer): The base of the sequence to be used for the zero coordinate of the first window. For simplicity, internal coordinates are used: the sequence begins at base 1. MinimumWindowSize (integer): The shortest window to use for the computations. MaximumWindowSize (integer): The longest window to use for the computations. SpaceBetweenWindows (integer): Windows are spaced so as to not collide. You can add extra distance with this parameter. If it is negative, the windows will overlap. NumberofWindows (integer): The number of windows to use for each computation. * The program will object if any of these parameters cause a window to go outside the sequence. xyin: output of this program, input to the xyplo graphics program. columns: 1: window size 2: Rs, Rsequence, bits 3: SD, Standard Deviation of Rs, bits 4: Rs/(window size), bits/base 5: SD/(window size), bits/base output: messages to the user description A window size is chosen. The first sequence in the book is broken into fragments of this size. These are aligned and the information content, Rsequence (Rs) is computed. This process is repeated for a range of window sizes defined in the parameters. The output is a data file (xyin) containing columns for window size (w), Rs and the standard deviation of Rs (SD). There are also two normalized columns for Rs/w and SD/w, which are reports in bits per base. Repeating structures will appear as peaks in a graph of Rs/w versus w. examples documentation [1996 April 8] see also lidel.p, winscan.p, delila.p, encode.p, rseq.p, xyplo.p author Thomas Dana Schneider bugs The program should produce a xyplop so that it can put the genomic information on the curve automatically. technical notes Paremeter dnamax must be set as large as possible so that the entire sequence can fit into a single array and therefore be accessed as rapidly as possible. Since Delila stores sequences with 2 bits/base (assuming a good compiler) so one can compute the size of the array in bytes. *) (* end module describe.winrs *) {This manual page was created by makman 1.44}

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