| Name |
ISOCHORE |
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| Status |
The current release has 0
entries and was indexed 10-Sep-2004.
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| Creation date |
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| Description |
ISOCHORE application details page
Plots isochores in large DNA sequences
The nuclear genomes of vertebrates are mosaics of isochores, very longstretches (>300kb) of DNA that are homogeneous in base composition andare compositionally correlated with the coding sequences that theyembed. Isochores can be partitioned in a small number of families thatcover a range of GC levels (GC is the molar ratio of guanine+cytosine inDNA), which is narrow in cold-blooded vertebrates, but broad inwarm-blooded vertebrates. This application plots GC content over a sequence. It is intended forlarge sequences such as complete chromosomes or large genomic contigs,although interesting results can also be obtained from shortersequences.
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| Literature |
- 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
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| WWW |
www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/isochore.html
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| Ftp |
The latest version of the EMBOSS package is available on
ftp://ftp.uk.embnet.org/pub/EMBOSS/
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| Contact |
This application was written by Peter Rice (pmr@sanger.ac.uk) InformaticsDivision, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton,Cambridge, CB10 1SA, UK.
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| See also |
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BTWISTED
| Calculates the twisting in a B-DNA sequence
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CHAOS
| Create a chaos game representation plot for a sequence
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COMPSEQN
| Counts the composition of dimer/trimer/etc words in a sequence
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DAN
| Calculates DNA RNA/DNA melting temperature
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FREAKN
| Residue/base frequency table or plot
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WORDCOUNT
| Counts words of a specified size in a DNA sequence
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| Data-fields in SRS |
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| Loaders |
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| SRS Description |
Structure
(
srsgen.i
,
srsdb.i
,
href.i
)
Syntax
Information
|