[ensembl-dev] coordinate-system 'group' versus 'chromosome'

[Anne Parker]

As I understand it, this nomenclature is specific to the stickleback community - they are in effect chromosomes, but we use the preferred terminology in Ensembl. Perhaps someone more knowledgeable can explain further?

Cheers

Anne


On 6 Aug 2012, at 11:39, PATERSON Trevor wrote:

> Could someone clarify the significance of naming a top-level coordinate-system as ‘group’ rather than ‘chromosome’?
>  
> There is one species (stickleback) in Ensembl that has a top-ranked coordinate system called ‘group’, rather than ‘chromosome’.
>  
> There is a karyotype page for stickleback and these ‘groups’ are described as chromosomes: there is no indication of what significance the name ‘group’ has.
>  
> I cannot find any other coordinate system called ‘group’, but in EnsemblGenomes the top ranked coord-system of  Drosophila pseudoobscura is named ‘chr-group’ but these do not seem to treated as chromosomes/karyotypes by the web interface.
>  
> I don’t think there is an enumeration of allowed coordinate-system names, with definitions  - maybe there could be?
>  
> cheers
>  
> trevor
>  
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org