Delila Program: consensus

consensus program

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

{   version = 1.17; (* of consensus.p 2005 May 26}

(* begin module describe.consensus *)
(*
name
   consensus: convert symvec to consensus to point out flaws in consensus

synopsis
   consensus(symvec: in, consensusp: in,
             list: out, conmarks: out, output: out)

files

   symvec:  a file that contains base frequency information for a protein
      or DNA binding site.

   list:  Processing of the symvec to show how the consensus model
      destroys data.

   conmarks:  consensus sequences in marks format for putting onto
      a sequence logo.  This requires the ShiftLettering function
      provided in marks.lettering.  Concatenate marks.lettering
      to conmarks to get the marks file of makelogo.  That is, in unix:

      cat marks.lettering conmarks > marks

   consensusp:  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.

      The second line contains two integers:
         fromrange: integer; the 5' or N terminus of the range to display
         torange: integer; the 3' or C terminus of the range to display

      The third line contains one real number for the cutoff below which
         a base is labeled 'n'.

   output: messages to the user

description

   How bad is the TATAAT consensus?  What are the relative fractions?
   The program is designed to allow one to look at a consensus sequence.
   Its purpose is to ATTACK THE CONCEPT OF CONSENSUS sequences.
   Do not use this program to publish a consensus sequence without indicating
   that the consensus sequence method is highly flawed!

examples

documentation

   T. D. Schneider, Consensus Sequence Zen,
   Applied Bioinformatics, 1 (3), 111-119, 2002.
   See link below.

see also

   example parameter file: consensusp

   Source of ShiftLettering function: marks.lettering

   Programs that make symvec files: alpro.p dalvec.p

   If you are tempted to use this program to publish something, DON'T!!!
   Read this:
   http://www.lecb.ncifcrf.gov/~toms/glossary.html#consensus_sequence
   and the Consensus Sequence Zen paper:
   http://www.lecb.ncifcrf.gov/~toms/paper/zen/

   Use these programs instead:
   make a sequence logo: makelogo.p
   make sequence walkers: makewalker.p

   If you don't know what those programs do, "go look it up":
   sequence logos:
   http://www.lecb.ncifcrf.gov/~toms/glossary.html#sequence_logo
   sequence walkers:
   http://www.lecb.ncifcrf.gov/~toms/glossary.html#sequence_walker

   This is a sequence logo:
   image for donor.pure

   This is a sequence walker:
   image for donorwalkersmall

   Examples of What You Miss (!) If You Use A Consensus Sequence:
   http://www.lecb.ncifcrf.gov/~toms/papers/splice/
   http://www.lecb.ncifcrf.gov/~toms/papers/walker/walker.html#fig2
   http://www.lecb.ncifcrf.gov/~toms/papers/baseflip/
   http://www.lecb.ncifcrf.gov/~toms/papers/repan3/

author

   Thomas Dana Schneider

bugs

   This program could be used by some foolish idiot to make a consensus and
   publish it!

   Well, ok, you can if your purpose is to attack the concensus sequence
   concept.  Otherwise, please read the 'see also' section above.

technical notes

*)
(* end module describe.consensus *)
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