Delila Program: rsconv

rsconv program

Documentation for the rsconv program is below, with links to related programs in the "see also" section.

{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 *)
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