Delila Program: rean

rean program

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

{   version = 1.02; (* of rean.p 2005 Jan 14}

(* begin module describe.rean *)
(*
name
   rean: list new RBS sites and determine if they are in frame with old sites

synopsis
   rean(oinst: in, data: in, dataout: out, strongestinst: out, output: out)

files

   oinst:  inst that defines the start and stop coordinate of a gene.

   data:  output of the biscan program.

   reanp:  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.

   dataout: an organized table of locations of ribosome binding sites
         found by biscan, along with new gene length orientation etc.

   strongestinst: makes inst file of the RBS with the highest
     information content.  The information content is reported in
     comments.

description

   This program analyzes the output of biscan and finds the RBS with
   the highest information content and the RBS that is closest to the
   start provided in oinst (annotated start).  This program is useful
   for reannotation.

examples

   {The parameter file is checked but not otherwise used: } reanp

documentation

see also

author

   Brent Michael Jewett

bugs

   strongestinst is hardwired to be -30 to +20; this should be read
   from the parameters

   The global variables should be in themain.

technical notes

   oinst file must be in the following format

   get from 123 +45 to 678 -910 direction -;

*)
(* end module describe.rean *)
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