Delila Program: alword

alword program

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

{version = 2.07; (* of alword.p 1992 June 4}

(* begin module describe.alword *)
(*
name
   alword: frequency and information of aligned words

synopsis
   alword(words: in, symvec: out, output: out)

files
   words:  Aligned words.  Since the input is usually to be a UNIX dictionary,
      there need not be any header lines.  However, if they exist, they must
      begin with an asterisk '*'.

      The remaining lines are used for the words.

   alwordp: parameters to control the program.  If the file is empty
      defaults are used.
      If the first line begins with the letter `e' then the words are
      aligned by their last character.
      If there is a first line, the second line must have the maximum
      word length to be included in the calculation.  Words longer than
      this will be skipped (and reported to output).

      If the first character of the second line is 'a' then all of the
      words in the file will be read.  Otherwise, only the first
      word on each line will be read.
   symvec:  table of frequencies and information content.  The information
      measure is corrected for small sample size (Schneider et al, 1986).
   output: messages to the user

description
   Take an aligned set of protein sequences and produce input to the
   consensus program for producing a logo.

examples

* This is an example sequence.
AGGEGCTT.
* This is the second example sequence.
* It is the last one.
YLREBS.

documentation
   Jotun Hein, Methods of Enzymology 183 (1990)
   Schneider et al. JMB 188:415 (1986)

see also
   alpro.p, makelogo.p

author
   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.alword *)
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