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{ version = 3.26; (* of compan.p 2015 Apr 26} (* begin module describe.compan *) (* name compan: composition analysis. synopsis compan(cmp: in, anal: out, companp: in, output: out) files cmp: the input composition, which is the output of program comp; anal: the output analysis of this program; companp: for parameters; should contain a single integer which specifies the maximum level for which the composition is analyzed. the maximum allowed level is 4, or the maximum level for which the composition was determined. output: for user messages; description calculates chi squared from a composition using: 1) assumption of equal frequencies to calculate mono, di, tri and tet expecteds; 2) mono frequencies to calculate di, tri and tet expecteds; 3) di frequencies to calculate tri and tet expecteds; 4) tri frequencies to calculate tet expecteds; the partial chi squared values are given for each oligo. The 'uncertainty' of the composition is also calculated, using the standard information theory definition: H = -sum(frequency * log(frequency)), where the sum is over each oligonucleotide of a given length and the log is taken to the base 2. This gives the uncertainty in bits. (Note: This was called 'information by Gary Stormo originally. However it is not the information, it is the uncertainty.) see also comp.p author Gary Stormo, corrected by Thomas Schneider bugs the program cannot do calculations for compositions larger than 4 *) (* end module describe.compan *) {This manual page was created by makman 1.45}{created by htmlink 1.62}