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

[Will Chow]

I believe Anne is correct in that its from the stickleback community, and the numbers represents the linkage groups.

http://www.nature.com/nature/journal/v414/n6866/fig_tab/414901a_F2.html

In UCSC genome browser they just substituted the groups with chr.

"The v1.0 stickleback genome has been sequenced to approximately 6X coverage. An estimated 87% of the sequence has been anchored to chromosomes (chrI - chrXXI). Of the remaining unanchored scaffolds, those that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn" with 1000 bp gaps between scaffolds. The stickleback mitochondrial sequence is also available as the virtual chromosome "chrM". "

I believe you can name whatever you want as toplevel via the seq_region_attrib/attrib_type toplevel attrib anyways.  I've done this with seq_regions labelled as super_scaffolds for my toplevel. 

Will


On 6 Aug 2012, at 11:45, Anne Parker wrote:

> 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
>> Bioinformatics 
>> The Roslin Institute
>> Royal (Dick) School of Veterinary Studies
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> 
> Anne Parker
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