Delila Program: localbest

localbest program

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

{   version = 1.22; (* of localbest.p 2005 May 26}

(* begin module describe.localbest *)
(*
name
   localbest: find features with the highest Ri in a given sequence range

synopsis
   localbest(features: in, localbestp: in, bestfeatures: out,
             lowerfeatures: out, output: out)

files
   features:  A list of locations of binding sites and other features.

   bestfeatures:  A list of the features from the original file which have the
      highest Ri in a given range

   localbestp:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      window:  Features are discarded if the coordinate of another feature with
         a higher Ri is less than the window distance away from the one being
         looked at.  Note that if window is 100, the region accepted will be
         2*100+1 = 201 bases.

      asterisks: If character is 'A' then the filtered out features are shown
         as asterisks in a lowerfeatures file.

   lowerfeatures:  A list of the features from the original file which have the
      lower Ri values in a given range. These are the features which have been
      'discarded' by the program.

   output: messages to the user

description

   Scan often produces a features file with many sites picked up over
   a small  range. This makes the map very difficult to look at, so
   this program  attempts to filter the features and find the one with
   the highest Ri over a  small range and only keep that one.

   The user should be aware that this program discards valuable
   information in  the form of possible binding sites.  For this
   reason, it is a good idea to  not set the window at more than 1
   helix turn (10.6 bp). Sites at this  distance apart are probably
   significant and should be kept in the features  file.

examples

documentation

see also
   lister.p, scan.p

author
   Elaine Bucheimer

bugs

technical notes

*)
(* end module describe.localbest *)
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