
                              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
