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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) 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 |
[-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, png | 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 |
---|---|
banana | Bending and curvature plot in B-DNA |
btwisted | Calculates the twisting in a B-DNA sequence |
chaos | Create a chaos game representation plot for a sequence |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
dan | Calculates DNA RNA/DNA melting temperature |
freak | Residue/base frequency table or plot |
wordcount | Counts words of a specified size in a DNA sequence |