Delila Program: dotmat

dotmat program

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

{version = 3.08; (* of dotmat 1994 sep 5 *)}

(* begin module describe.dotmat *)
      dotmat: dot matrices of two books

      dotmat(xbook: in, ybook: in, mlist: out, dotmatp: in, output: out)

      xbook: a book from the delila system

      ybook: a book from the delila system

      mlist: a dot matrix for each sequence pair between the two books.
         the "dots" are printed as numbers:
            1 means gt base pair
            2 means at base pair
            3 means gc base pair
         xbook sequences are written down the page and those of
         ybook go across the page.
         if mlist is wider than your printer, use the split program.

      dotmatp: parameters to control the mlist.
         if dotmatp is empty, default values are used.  otherwise
         if the first line begins with a "g" then g-u pairs are printed.

      output: messages to the user

      dotmat produces a dot matrix for all complementary base pairs
      between all pairs of sequences in the two books.  because a list of
      helices is not made, the program is much more efficient for short
      minimum helices than is the pair of programs helix and matrix.

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

see also
      helix.p, matrix.p, split.p

      thomas d. schneider

      none known

(* end module describe.dotmat *)
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