EMBOSS: freak


Program freak

Function

Residue/base frequency table or plot

Description

freak takes one or more sequences as input and a set of bases or residues to search for. It then calculates the frequency of these bases/residues in a window as it moves along the sequence. The frequency is output to a data file or (optionally) plotted.

The default set of bases is 'cg' which will calculate the frequency of 'G' + 'C' bases within the default moving window of 30 bases.

Usage

Here is a sample session with freak:

% freak embl:hsfau 
Residue/base frequency table or plot
Residue letters [gc]: 
Output file [hsfau.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

Input file format

Normal sequence USAs.

Output file format

The output from the above example is:


FREAK of HSFAU from 1 to 518 Window 30 Step 1

1          0.500000
2          0.533333
3          0.566667
4          0.533333
5          0.533333
6          0.566667
7          0.566667
8          0.566667
9          0.600000
10         0.633333
11         0.633333
12         0.666667
13         0.666667
14         0.666667
15         0.666667
16         0.633333
17         0.666667
18         0.633333
19         0.633333
20         0.633333
21         0.666667
22         0.666667
23         0.700000
24         0.733333
25         0.700000
26         0.666667
27         0.633333
28         0.600000
29         0.566667
30         0.600000
31         0.633333
32         0.600000
33         0.600000
34         0.633333
35         0.600000
36         0.600000

[listing truncated for brevity]

The ouput consists of a title line and then two columns containing the position of the start of the window and then the frequency in that window of the bases or residues being searched for.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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
cuspCreate a codon usage table
geeceeCalculates the fractional GC content of nucleic acid sequences
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 Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Wriiten (Aug 2000) Alan Bleasby

Target users

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

Comments