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EMBOSS: wobble |
% 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 |
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 | 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 |
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 |
freak | Residue/base frequency table or plot |
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 |
tfscan | Scans DNA sequences for transcription factors |
wordcount | Counts words of a specified size in a DNA sequence |