Delila Program: clual

clual program

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

{version = 1.08; (* of clual.p 2002 Feb 19}

(* begin module describe.clual *)
(*
name
   clual: clustal to alpro conversion

synopsis
   clual(clustalout: in, clualp: in, protseq: out, output: out)

files

   clustalout:  output of the CLUSTAL program

   protseq:  input to the alpro program

   clualp:  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 of clualp must match the first line
      of the clustalout file.  This is used to check that
      the clustalout file is correct.

      verbose (character): If the first character of the third line is
      a 'v' then the program will name the segment numbers as it reads it in,
      and then give the name of each sequence as it is written out.

   output: messages to the user

description

   Convert from CLUSTAL format to allow one to present COG output
   as a sequence logo.  The CLUSTAL format is broken up into segments.
   Alpro requires continuous sequences.  This program rearranges the
   CLUSTAL data to the form alpro needs.

examples

   The first line of a clustal file looks like this:

CLUSTAL W (1.74) multiple sequence alignment

   This is used to check that the input is good.

documentation

see also

example parameter file: clualp

program that uses the output of this program: alpro.p
program that finally generates the sequence logo: makelogo.p

COG: http://www.ncbi.nlm.nih.gov/COG/
COG: ftp://ncbi.nlm.nih.gov/pub/COG/

an example alignment:
http://www.ncbi.nlm.nih.gov/COG/aln/COG0526.aln

the entire list of alignments, ready to grab:
ftp://ncbi.nlm.nih.gov/pub/COG/aln/

wget can be used to grab the alignments:
http://www.lecb.ncifcrf.gov/~toms/wget.html

Why one should not use consensus sequences:
http://www.lecb.ncifcrf.gov/~toms/glossary.html#consensus_sequence

author

   Thomas Dana Schneider

bugs

technical notes

   The clustal format has waste spaces.  If "_" represents a space,
   then we have at the boundary of two segments:

YPR082c_________------------------------------------------------------------
____________________________________________________________________________
_
BS_resA_________------------------

   This program ignores the spaces, but one wonders why they are there ...
   AH!!!  These contain STUPID consensus sequences!!!
   The program will ignore this idiotic data line.

*)
(* end module describe.clual *)
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