Function

Description

isochore plots GC content in windows over a DNA sequence. The data may also be written to output file. The window wize and shift increment (the number of bases separating the start of each window) may be specified. isochore is suitable for use with 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

Output file format

Data files

Notes

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.

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

Author(s)

History

Target users

Comments