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 nameDescription
bananaBending and curvature plot in B-DNA
btwistedCalculates the twisting in a B-DNA sequence
chaosCreate a chaos game representation plot for a sequence
compseqCounts the composition of dimer/trimer/etc words in a sequence
danCalculates DNA RNA/DNA melting temperature
freakResidue/base frequency table or plot
wordcountCounts 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