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EMBOSS: isochore |
This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences.
% isochore Input sequence: tgb:scchriii Output file [scchriii.iso]:click here for result
Mandatory qualifiers: [-sequence] sequence Sequence USA [-out] outfile Output file name -graph xygraph Graph type Optional qualifiers: -window integer Window size -shift integer Shift increment Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-out] (Parameter 2) |
Output file name | Output file | <sequence>.isochore |
-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 |
Optional qualifiers | Allowed values | Default | |
-window | Window size | Integer 1 or more | 1000 |
-shift | Shift increment | Integer 1 or more | 100 |
Advanced qualifiers | Allowed values | Default | |
(none) |
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 |
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 |
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 |