
                                EMBOSS: cusp
     _________________________________________________________________
   
                                 Program cusp
                                       
Function

   Create a codon usage table
   
Description

   Reads one or more coding sequences (CDS sequence only) and calculates
   a codon frequency table.
   
   The output file can be used as a codon usage table in other
   applications.
   
Usage

   Here is a sample session with cusp, using just one sequence. Normal
   use would be to extract a set of coding sequences and to use these as
   input.

% cusp -sbeg 135 -send 1292
Create a codon usage table
Input sequence: embl:paamir
Output file [paamir.cusp]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -cfile              codon      Codon usage table name

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.cusp
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -cfile Codon usage table name Codon usage file in EMBOSS data path
   Ehum.cut
   
Input file format

Output file format

   Here is the start of the output from the example run, which used a
   single CDS from Pseudomonas aeruginosa which has a very high GC
   content ands a strong coding bias, as shown by the codons for Alanine
   where those ending with G or C are used almost exclusively.

# CUSP codon usage file
# Codon Amino acid      Fract   /1000   Number
GCA     A               0.077   7.772   3
GCC     A               0.462   46.632  18
GCG     A               0.462   46.632  18
GCT     A               0.000   0.000   0

.........

   The 'Fract' column gives the faction of all amino acids coded for by
   this codon triplet.
   
   The /1000 column represents the number of codons, given the input
   sequence(s), there are per 1000 bases. This will be an extrapolation
   if the sequence is shorter than 1000 bases.
   
   If multiple sequences are input then the statistics are given for all
   of the sequences together, not individually.
   
Data files

   cusp reads a codon usage file, but only as a template and does not use
   any of the data so any file will give the same results.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   Always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                  Description
   cai          CAI codon adaptation index
   chips        Codon usage statistics
   codcmp       Codon usage table comparison
   syco         Synonymous codon usage Gribskov statistic plot
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Spring 2000 - written
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
