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 *)
   localbest: find features with the highest Ri in a given sequence range

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

   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


   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.



see also
   lister.p, scan.p

   Elaine Bucheimer


technical notes

(* end module describe.localbest *)
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