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EMBOSS: chaos |
Starting from the middle, move half way to the corner of the box representing the first base in the sequence and draw a dot.
Then for each subsequent base move half way to the corresponding box corner and draw a dot.
Finally display the number and percentage values of AGCT bases.
chaos embl:eclacclick here for result
Mandatory qualifiers (* if not always prompted): [-sequence] sequence Sequence USA * -graph graph Graph type * -outfile outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -data bool Display as data |
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 |
-outfile | Output file name | Output file | <sequence>.chaos |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-data | Display as data | Yes/No | No |
Program name | Description |
---|---|
chips | Codon usage statistics |
codcmp | Codon usage table comparison |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
cpgplot | Plot CpG rich areas |
cpgreport | Reports all CpG rich regions |
cusp | Create a codon usage table |
diffseq | Find differences (SNPs) between nearly identical sequences |
dotmatcher | Displays a thresholded dotplot of two sequences |
dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
einverted | Finds DNA inverted repeats |
equicktandem | Finds tandem repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
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 |
palindrome | Looks for inverted repeats in a nucleotide sequence |
polydot | Displays all-against-all dotplots of a set of sequences |
redata | Search REBASE for enzyme name, references, suppliers etc |
restrict | Finds restriction enzyme cleavage sites |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |
tfscan | Scans DNA sequences for transcription factors |
wobble | Wobble base plot |
wordcount | Counts words of a specified size in a DNA sequence |
Completed 22nd March 1999. Last modified 14th June 1999.