By downloading this code you agree to the
Source Code Use License (PDF). |
{version = 1.19; (* of rsconv.p 1998 June 10} (* begin module describe.rsconv *) (* name rsconv: Compute the convolution between two rsdata files. synopsis rsconv(rsdata1, rsdata2: in, rsconvp: in, xyin: out, rsconvmax: out, output: out) files rsdata1, rsdata2: rsdata files from the rseq program rsconvp: parameters to control the program. The file must contain the following parameters, one per line: parameterversion: The version number of the program. This allows the user to be warned if an old parameter file is used. convolutionmethod: A single character that determines how the convolution is performed: m(ultiplication) or c(orrelation) xyin: input to the xyplo program for graphing. columns: 1: point definition: d(ata) p(eak) 2: coordinate 3: convolution value rsconvmax: maximum convolution value (one real) output: messages to the user description Rsconv will convolve two information curves by one of two methods: multiplication: The two Rsequence(l) vectors are set at various relative positions. Each corresponding pair of positions is then multiplied together and summed, to get total bits squared for a particular offset. This is the dot product of the two information curves represented as vectors. The cosine of the angle between them is then found by dividing by the magnitude of each vector. correlation: The standard correlation coefficient is computed for the overlapping region The convolution method can't use the actual bases since they differ. Individual information can be used instead for comparisons based on sequence matching. When looking for a relationship between human acceptor and E. coli ribosome binding site, we don't want to get large hits by doing the acceptor to the T7 promoters. Either normalization takes care of this. examples Example files are listed below. The file rsconv.xyplop is used for standard runs. Change the zzz to the appropriate pair. This can be done conveniently in Unix with sed: cat rsconv.xyplop | sed -e "s/zzz/name/" | cat > xyplop documentation see also rseq.p, xyplo.p, rsconvp, rbs1055.rsdata, spliceA.rsdata, rsconv.xyplop author Thomas Dana Schneider bugs The largest combined size of the two Rs(l) vectors is given by constant maxposition. technical notes *) (* end module describe.rsconv *) {This manual page was created by makman 1.45}{created by htmlink 1.62}