Delila Program: hist

hist program

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

{version = 4.27; (* of hist.p 1994 sep 6}

(* begin module describe.hist *)
      hist: make a histogram of aligned sequences.

      hist(inst: in, book: in, hst: out, histp: in, output: out);

      inst: the instructions which generated the book, used to
            align the sequences; the format of the instructions must be
            'get from # -x to # +y;' - the alignment is done on the base #.
            if this file is empty the sequences are aligned by their 5
            prime ends.
      book: the sequences, not longer than 'dnamax' (see technical note);
      hst: the histogram table, giving the position occurence
            of all oligonucleotides from oligomin to oligomax  in length
            (see file histp).  note - if the histogram is wider than can
            be printed on a page, use the program split to print hst.
      histp: to set the length of oligonucleotides searched for; contains two
            integers, one per line, the first specifying oligomin
            (the length of the shortest oligonucleotide which is searched for),
            the second oligomax (the longest oligonucleotide searched for,
            which cannot be greater than 4);
            note: if oligomin is zero, then the bases are counted.
      output: for error messages.

      makes a histogram of the occurences of oligonucleotides at positions
      relative to some aligned base.  this is done for all oligonucleotides
      with lengths from  'oligomin' to 'oligomax', set by file histp.

see also
      split.p, alist.p, histan.p

      gary stormo

      none known

technical note
      the constant 'dnamax'  from the module book.const may be too
      large for efficient use of this program.  if you do not expect to do
      histograms on aligned sequences of greater than, say, 120 nucleotides
      you can go into the source program (hists) and change 'dnamax' before
(* end module describe.hist *)
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