Delila Program: patser

patser program

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

{version = 2.32; (* of patser.p 1994 sep 5}

(* begin module describe.patser *)
(*
name
      patser: pattern searcher

synopsis
      patser(book: in, pattern: in, scale: in, patserp: in,
             values: out, inst: out, output: out)

files
      book: the book of sequences to be searched. only numbered sequences are
         searched.
      pattern: the pattern used to search with. this is the output of the
         pattern learning program, patlrn.
      scale: contains one integer, by which the values should be divided
         to bring them into the correct scale if a matrix from rseq was used.
      patserp: parameter file, to set the value of 'printmin', the minimum
         value of a site in order for it to be identified in the file 'values'.
         if this file is empty, 'printmin' is set to the functional sequence
         minimum of the pattern matrix.
      values: the sites, and their values, which are evaluated above 'printmin'.
      inst: the instructions to get the regions around the sites identified
         in the file 'values'.  the region obtained is identical to the pattern
         used in the search.
      output: for messages to the user.

description
      patser uses a pattern matrix, the output of the pattern learning program
      patlrn, to search a book of sequences.  each base in each sequence is
      used as the 'aligned base', and the sites which are evaluated above
      'printmin' are identified in the file 'values'.  instructions which can
      be used to obtain those sites, and the nucleotides around them over the
      region contained in the pattern matrix, are put into the file 'inst'.

      NOTE: if the pattern is off the end of the sequence it is
      nolonger reported.

see also
      patrln.p, patval.p

author
      gary d. stormo (modified by tom schneider)

bugs
      none known
*)
(* end module describe.patser *)
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