Delila Program: helix

helix program

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

{      version = 3.24; (* of helix 1994 sep 5}

(* begin module describe.helix *)
(*
name
   helix: find helices between sequences in two books

synopsis
   helix(xbook: in, ybook: in, hlist: out, helixp: in, output: out)

files
   xbook: a book from the delila system
   ybook: a book from the delila system
   hlist: a list of helices between pieces in xbook and ybook.
      the first line is the program identification
      the second two lines are the x and y book titles
      the third line gives the minimum length or the maximum energy
          of helixes recorded
      the fourth line states whether or not g-u pairs are allowed
      the fifth line states whether or not energies are printed
      the following lines are the helices
      breaks between sequences are indicated.
   helixp: parameters that control the helix list.
      if helixp is empty, default values are used.
      otherwise, the file must contain three lines:
      1. if this number is a positive integer, it specifies the minimum length
         in base pairs of the helixes written in hlist.  if it is a negative
         real number, it specifies the maximum energy in kcal of the helixes
         written.
      2. if the first character is a "g" then g-u pairs are allowed,
         otherwise not.
      3. if the first character is an "e" then the energy of each helix
         will be written in hlist.
   output: messages to the user

description
   All sequences in xbook are compared to all sequences in ybook.
   The complementary helices (of some minimum length and longer or of
   some maximum energy or less) are listed in hlist by the 5' ends of the
   helix on both sequences.  This information, along with the length of
   the helix, determines the location of the helix.  One can allow g-u
   pairing if desired.  If the helix lengths desired are very short,
   it is better to use dotmat (see "technical notes" below).
      The new Rules are now used to calculate the helix.

documentation
   delman.use.comparison

   J. V. Maizel, Jr. and R. P. Lenk PNAS 78: 7665-7609 (1981)

   Tinoco et al. Nature New Biology vol 246 pp 40-41, 1973.

   S. M. Freier, R. Kierzek, J. A. Jaeger, N. Sugimoto,
   M. H. Caruthers, T. Nelson, and D. H. Turner,
   "Improved free-energy paramters for predictions of RNA duplex stability"
   PNAS 83: 9373-9377 (1986)

see also
   matrix.p, dotmat.p, keymat.p

author
   Thomas D. Schneider

bugs
   GU pairs and bulges are not done using the new data.
   An option for pair-wise (rather than multiplicative) comparisons
   of sequences would be nice.

technical notes
   The shortest length helix ever recorded in hlist is determined
   by the constant absminlength.  This overrides the parameters.

*)
(* end module describe.helix *)
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