| ## EMBOSS: isochore

# Program isochore

## Function

Plots isochores in large DNA sequences

## Description

The nuclear genomes of vertebrates are mosaics of isochores, very long stretches (>300kb) of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels (GC is the molar ratio of guanine+cytosine in DNA), which is narrow in cold-blooded vertebrates, but broad in warm-blooded vertebrates.

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.

## Usage

Here is a sample session with isochore. This reads yeast chromosome 3 from a remote web server so the sequence reading may take a little time.

    % isochore
    Input sequence: tgb:scchriii
    Output file [scchriii.iso]:

click here for result

## Command line arguments

       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                bool       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)

## Input file format

## Output file format

The graph from the example run

## Data files

## Notes

## References

1. Bernardi G Isochores and the evolutionary genomics of vertebrates. Gene 2000 Jan 4;241(1):3-17
2. Pesole G, Bernardi G, Saccone C Isochore specificity of AUG initiator context of human genes. FEBS Lett 1999 Dec 24;464(1-2):60-2
3. Bernardi G The human genome: organization and evolutionary history. Annu Rev Genet 1995;29:445-76

## Warnings

## Diagnostic Error Messages

## Exit status

## Known bugs

## See also

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

## Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments