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{ version = 5.41; (* of rseq.p 2005 Sep 21} (* begin module describe.rseq *) (* name rseq: rsequence calculated from encoded sequences synopsis rseq(encseq: in, cmp: in, rsdata: out, output: out) files encseq: the output of the encode program cmp: a composition from the comp program. if cmp is empty, then equal frequencies are assumed. rsdata: a display of the information content of each position of the sequences, with the sampling error variance. This output is ready to be used as input to rsgra or as data for genhis for plotting. output: messages to the user. description Encoded sequences from encseq are converted to a table of frequencies for each base (b) at each aligned position (l). rsequence(l) and the variance var(hnb) are calculated and shown along with their running sums. rsequence and the variance due to sampling error are shown for the whole site, but the running sums let one find rsequence and the variance for any subrange desired. n, the number of example sequences may vary with position, so both n and e(hnb) are shown. documentation Schneider, T.D., G.D. Stormo, L. Gold and A. Ehrenfeucht (1986) The information content of binding sites on nucleotide sequences. J. Mol. Biol. 188: 415-431. see also INPUT the program that makes the input encseq file: encode.p the program that makes the input cmp file: comp.p OUTPUT: the program that uses the rsdata file for making logos: dalvec.p GRAPHICS: a program to make a graph of the curve (old): rsgra.p another program to make a graph of the curve: xyplo.p RELATED: a program to compute the small sample error: calhnb.p a related program to compute frequencies: encfrq.p author Thomas D. Schneider bugs Does not handle di-nucleotides or longer oligos technical notes Constants maxsize (procedure calehnb) and kickover (procedure makehnblist) determine the largest n for which e(hnb) is used. Above this, ae(hnb) is used. Do not set these below 50 without careful analysis. Other constants are in module rseq.const. *) (* end module describe.rseq *) {This manual page was created by makman 1.45}{created by htmlink 1.62}