isochore
Function
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
Command line arguments
Input file format
isochore reads a normal nucleic acid USA.
Output file format
Data files
None.
Notes
None.
References
-
Bernardi G
Isochores and the evolutionary genomics of vertebrates.
Gene 2000 Jan 4;241(1):3-17
-
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
-
Bernardi G
The human genome: organization and evolutionary history.
Annu Rev Genet 1995;29:445-76
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with a status of 0.
Known bugs
None.
Author(s)
History
Target users
Comments