Delila Program: rep

rep program

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

{version = 1.75; (* of rep.p 1995 July 26}

(* begin module describe.rep *)
(*
name
      rep: records repeats between sequences in two books

synopsis
      rep(hlist: in, xbook: in, ybook: in,
             fout: out, pout: out, repp: in, output: out)

files hlist: a list of helices for xbook and ybook generated
             by the program helix.
      xbook: a book from the delila system.
      ybook: a book from the delila system.
      fout:  a file containing the following information about each repeated
         sequence that satisfies the criteria of repp:
         *  the 5 prime ends of the two occurrences of the repeat.
         * rlength, length of the repeated sequence.
         * distance: if direct repeats, the number of bases from five prime end
            to five prime end of each repeat; if inverted repeats, the number
            of bases from three prime end to five prime end (i.e., pseudo-loop
            distance). in every case, the smallest possible distance is given.
      pout: a file containing information about palindromes (only filled when
            inverted repeats are found in related sequences, see below).
      repp: input parameter file, must contain 3 characters, one per line.
               this may be followed by 4 integers, one per line.
         * mode of repeat:
            d = direct repeat (xbook and ybook have opposite directions)
            i = inverted repeat (xbook and ybook are in the same direction)
         * the types of xbook and ybook used in helix program:
            u = unrelated (any two sequences - no distances are calculated)
            r = related (sequences derived from the same piece of dna. the
                coordinate numbering of both books must be the same in order
                to calculate distances.)
         * the energies of hlist reflect the composition of the repeat
            e = "energies" are to be reported
            n = no "energies" are to be reported
         * minimum number of bases in a repeat to be recorded.
         * maximum number of bases in a repeat to be recorded.
         * minimum distance between repeated sequences to be recorded.
         * maximum distance between repeated sequences to be recorded.
      output: messages to the user.

description
      rep uses information generated by the helix program to record the
      occurrences of repeated sequences of dna. helices are interpreted as
      repeats, direct or inverted depending upon the input sequences.
      repeats that meet the criteria of minimum length and minimum and/or
      maximum distance between half repeats are reported in fout.
      palindromes are reported in pout.

see also
      helix.p, matrix.p, keymat.p

author
      Britta Singer and Lane Wyatt

bugs  1.  when xbook and ybook have sequence in common, hlist reports
      each "helix" twice.  rep is able to eliminate duplicates only
      when xbook and ybook overlap completely.  thus in cases of
      partial overlap, some repeats may be duplicated.
      2.  rep uses external coordinates to calculate distances and will
      bomb with complicated coordinates. *)
(* end module describe.rep *)
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