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wobble |
For each of the six possible translation frames, this plots a graph showing the percentage of 'G' and 'C' bases in the third position of codons in the frame within a window that is moved over the sequence.
Bases other than 'G' and 'C' can be chosen with the -bases option.
The Mean of the third base percentage value is drawn as a horizontal line across the plots.
% wobble Wobble base plot Input sequence: embl:paamir Graph type [x11]: Output file [paamir.wobble]:click here for the result
Mandatory qualifiers: [-sequence] sequence Sequence USA -graph xygraph Graph type -outf outfile Output file name Optional qualifiers: -window integer Window size in codons Advanced qualifiers: -bases string Bases used General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-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, png | EMBOSS_GRAPHICS value, or x11 |
-outf | Output file name | Output file | <sequence>.wobble |
Optional qualifiers | Allowed values | Default | |
-window | Window size in codons | Integer 1 or more | 30 |
Advanced qualifiers | Allowed values | Default | |
-bases | Bases used | Any string is accepted | GC |
"Specifying ACG&T is meaningless" - When you use the option -bases to specify the bases to look for, it is pointless to specuy looking for all the possible bases as these should add to 100% all the time.
"No bases specified" - Similarly you have to specify soem bases to look for otherwise you must plot a 0% line.
Program name | Description |
---|---|
getorf | Finds and extracts open reading frames (ORFs) |
marscan | Finds MAR/SAR sites in nucleic sequences |
plotorf | Plot potential open reading frames |
showorf | Pretty output of DNA translations |