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                boolean    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.

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 nameDescription
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
newcpgreportReport CpG rich areas
newcpgseekReports 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