{ version = 3.76; (* of markov.p 2004 Sep 9}
(* 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.
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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