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EMBOSS: freak |
The default set of bases is 'cg' which will calculate the frequency of 'G' + 'C' bases within the default moving window of 30 bases.
% freak embl:hsfau Residue/base frequency table or plot Residue letters [gc]: Output file [hsfau.freak]:
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 |
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.
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 |