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

Jay Humphrey jhumphre at ebi.ac.uk
Mon Aug 6 12:08:47 BST 2012


I recently reviewed the way Ensembl fetches and renders sequence regions 
and discovered that labels like 'chromosome' and 'contig' are fixed, not 
configurable, and rendered in one particular way as a track (on pages 
with tracks displayed). The sequence region track has the fixed label 
'Contigs'. It displays your sequence level (lowest rank) coordinate 
system in alternating blue shaded regions and allows you to navigate by 
pop-up menu to a region centered on the contig.
-Jay

On 06/08/2012 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 <mailto:trevor.paterson at roslin.ed.ac.uk>
>
> Bioinformatics
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-- 
Jay Humphrey                   Ensembl Genomes Web Developer
EMBL-EBI                       Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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