EMBOSS: freak

Program freak

Function

Residue/base frequency table or plot

Description

Usage

Here is a sample session with freak:


% freak

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-seqall]            seqall     Sequence database USA
   -letters            string     Residue letters
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers:
   -step               integer    Stepping value
   -window             integer    Averaging window

   Advanced qualifiers:
   -plot               bool       Produce graphic

Mandatory qualifiers Allowed values Default

[-seqall]
(Parameter 1) Sequence database USA Readable sequence(s) Required

-letters Residue letters Any string is accepted gc

-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm EMBOSS_GRAPHICS value, or x11

-outfile Output file name Output file <sequence>.freak

Optional qualifiers Allowed values Default

-step Stepping value Any integer value 1

-window Averaging window Any integer value 30

Advanced qualifiers Allowed values Default

-plot Produce graphic Yes/No No

Mandatory qualifiers	Allowed values	Default
[-seqall] (Parameter 1)	Sequence database USA	Readable sequence(s)	Required
-letters	Residue letters	Any string is accepted	gc
-graph	Graph type	EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm	EMBOSS_GRAPHICS value, or x11
-outfile	Output file name	Output file	<sequence>.freak
Optional qualifiers	Allowed values	Default
-step	Stepping value	Any integer value	1
-window	Averaging window	Any integer value	30
Advanced qualifiers	Allowed values	Default
-plot	Produce graphic	Yes/No	No

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

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
cusp	Create a codon usage table
geecee	Calculates the fractional GC content of nucleic acid sequences
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)

History

Target users

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