Delila Program: rseq

rseq program

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

{   version = 5.41; (* of rseq.p 2005 Sep 21}

(* begin module describe.rseq *)
(*
name
      rseq: rsequence calculated from encoded sequences

synopsis
      rseq(encseq: in, cmp: in, rsdata: out, output: out)

files
      encseq: the output of the encode program
      cmp: a composition from the comp program.
          if cmp is empty, then equal frequencies are assumed.
      rsdata: a display of the information content of each position
         of the sequences, with the sampling error variance.
         This output is ready to be used as input to rsgra or as data
         for genhis for plotting.
      output: messages to the user.

description
      Encoded sequences from encseq are converted to a table of frequencies
      for each base (b) at each aligned position (l).  rsequence(l)
      and the variance var(hnb) are calculated and shown along with
      their running sums.  rsequence and the variance due to sampling
      error are shown for the whole site, but the running sums let one
      find rsequence and the variance for any subrange desired.
         n, the number of example sequences may vary with position, so
      both n and e(hnb) are shown.

documentation
      Schneider, T.D., G.D. Stormo, L. Gold and A. Ehrenfeucht (1986)
      The information content of binding sites on nucleotide sequences.
      J. Mol. Biol. 188: 415-431.

see also
      INPUT
      the program that makes the input encseq file: encode.p
      the program that makes the input cmp file: comp.p

      OUTPUT:
      the program that uses the rsdata file for making logos: dalvec.p

      GRAPHICS:
      a program to make a graph of the curve (old): rsgra.p
      another program to make a graph of the curve: xyplo.p

      RELATED:
      a program to compute the small sample error: calhnb.p
      a related program to compute frequencies: encfrq.p

author
      Thomas D. Schneider

bugs
      Does not handle di-nucleotides or longer oligos

technical notes
      Constants maxsize (procedure calehnb) and kickover (procedure
      makehnblist) determine the largest n for which e(hnb) is used.  Above
      this, ae(hnb) is used.  Do not set these below 50 without careful
      analysis.  Other constants are in module rseq.const.

*)
(* end module describe.rseq *)
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