
                               EMBOSS: geecee
     _________________________________________________________________
   
                                Program geecee
                                       
Function

   Calculates the fractional GC content of nucleic acid sequences
   
Description

   This calculates the fraction of G+C bases of the input nucleic acid
   sequence(s).
   
   It reads in nucleic acid sequences, sums the number of 'G' and 'C'
   bases and writes out the result as the fraction (in the interval 0.0
   to 1.0) of the length of the whole sequence.
   
Usage

   Here is a sample session with geecee.

% geecee embl:hhtetra
Output file [hhtetra.geecee]:

Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   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>.geecee
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Any DNA sequence USA.
   
Output file format

   Here is the output from the example usage:

#Sequence   GC content
HHTETRA       0.53

   The first non-blank line is the title line. Subsequent lines consist
   of two columns of data.
     * The first column is the name of the sequence.
     * The second column is the percentage G+C content of the sequence.
       
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 on successful completion.
   
Known bugs

   None.
   
See also

   Program name         Description
   cpgplot      Plot CpG rich areas
   cpgreport    Reports all CpG rich regions
   newcpgreport Report CpG rich areas
   newcpgseek   Reports CpG rich regions
   
Author(s)

   This application was written by Richard Bruskiewich
   (rbsk@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome
   Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
   
History

Completed 18th June 1999.
Last Modified 18th July 1999.

Target users

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