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{ 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 *) {This manual page was created by makman 1.45}{created by htmlink 1.62}