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)

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

Notes

References

Warnings

Diagnostic Error Messages

Exit status

0 on successful completion.

Known bugs

Program name	Description
chaos	Create a chaos game representation plot for a sequence
chips	Codon usage statistics
codcmp	Codon usage table comparison
compseq	Counts the composition of dimer/trimer/etc words in a sequence
cpgplot	Plot CpG rich areas
cpgreport	Reports all CpG rich regions
cusp	Create a codon usage table
freak	Residue/base frequency table or plot
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
wobble	Wobble base plot
wordcount	Counts 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.