Delila Program: markov

markov program

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

{   version = 3.77; (* of markov.p 2012 May 31}

(* begin module describe.markov *)
(*
name
      markov: markov chain generation of a DNA sequence from composition.

synopsis
      markov(cmp: in, mkvseqs: out, listing: out, markovp: in, output: out)

files
      cmp: the input composition, which is the output of program comp.
           If the file is empty, equiprobable mononucleotide
           composition is used.

      mkvseqs: the output dna sequences of this program.

      listing: contains the following information about program execution:
         program and version number.
         first three lines of the input composition file used to
            generate the sequences with.
         the four input parameters - number of sequences, length of sequences,
            the seed number, and the depth of sequence generation.
         a listing of any sequence that could not be generated from the
            prior length specified in the markovp file.
            the listing contains the sequence number, the sequence position
            and the depth of restart of sequence generation.

      markovp: for parameters; markovp must contain four numbers
         each on separate lines:
         1. number of sequences desired - an integer
         2. the length of each sequence - an integer
         3. a seed number between zero and one or outside this range
         if a computer date and time seed is desired.  the seed
         is used to start the random number generator. - a real
         4. the number of bases prior to the one about to be inserted
         which are to influence the choice of the base to be inserted.
         zero means equiprobable random sequences are desired.
         example:   20 number of sequences desired
                    100 length of sequences desired
                    2.0 for a computer date and time seed
                    3 composition depth used to generate next base

      output: for user messages.

description

      Markov generates a set of random dna sequences which have
      approximately the same composition as the one in the composition
      file supplied to the program.  The user chooses the depth of the
      composition to be used.  For example, if trinucleotides
      (composition depth = 3) are used, the previous two bases
      determine the probability of the next base in the sequence.
      This is called a markov chain.

      Sometimes the program will work itself into a corner, when no
      composition exists for the previous few bases.  In these cases,
      the program restarts with the longest possible oligonucleotide
      that does exist in the composition.  These cases are recorded in
      the listing.

see also
      comp.p, compan.p, rndseq.p

author
      John Eberwein, Gary Stormo, Tom Schneider

bugs
      none known
*)
(* end module describe.markov *)
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