{ 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:
https://alum.mit.edu/www/toms/glossary.html#consensus_sequence
and the Consensus Sequence Zen paper:
https://alum.mit.edu/www/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:
https://alum.mit.edu/www/toms/glossary.html#sequence_logo
sequence walkers:
https://alum.mit.edu/www/toms/glossary.html#sequence_walker
This is a sequence logo:
This is a sequence walker:
Examples of What You Miss (!) If You Use A Consensus Sequence:
https://alum.mit.edu/www/toms/papers/splice/
https://alum.mit.edu/www/toms/papers/walker/walker.html#fig2
https://alum.mit.edu/www/toms/papers/baseflip/
https://alum.mit.edu/www/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 *)
{This manual page was created by makman 1.45}
{