Delila Program: floc

floc program

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

{   version = 1.15; (* of floc.p 2005 May 30}

(* begin module describe.floc *)
(*
name
   floc: fast find features of highest Ri in a given sequence range

synopsis
   floc(features: in, flocp: 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

   flocp:  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.
         THIS FEATURE IS IGNORED in floc

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

         NEW: and the same for bestfeatures.

      maxsequences: The maximum number of sequences to process.
         If maxsequences < 0, all sequences will be processed.

      RangeFrom, RangeTo: the base range of the sequences to analyze.

   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

   Floc is a fast local best program.  The input is a list of features
   found by the scan program in a Delila book containing nucleic acid
   sequences.  The set of features for each sequence in the book are
   collected and the feature that has the highest Ri value is sent to
   the bestfeatures file, while the remainder are sent to the
   lowerfeatures file

   The window parameter is IGNORED: everthing in a single sequence is
   analyzed and the feature with the highest Ri is reported.

   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
   localbest.p  lister.p  scan.p

author
   Elaine Bucheimer wrote the original localbest.
   Thomas Schneider completely rebuilt the program for speed in floc.

bugs

technical notes

*)
(* end module describe.floc *)
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