EMBOSS: geecee


Program geecee

Function

Calculates the fractional GC content of nucleic acid sequences

Description

This calculates the percentage G+C of the input nucleic acid sequence(s).

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)

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

Notes

References

Warnings

Diagnostic Error Messages

Exit status

0 on successful completion.

Known bugs

See also

Program nameDescription
chaosCreate a chaos game representation plot for a sequence
chipsCodon usage statistics
codcmpCodon usage table comparison
compseqCounts the composition of dimer/trimer/etc words in a sequence
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
cuspCreate a codon usage table
freakResidue/base frequency table or plot
isochorePlots isochores in large DNA sequences
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions
wobbleWobble base plot
wordcountCounts words of a specified size in a DNA sequence

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