[ensembl-dev] 1-based coordinate system Vs 0-based coordinate system

Duarte Molha Duarte.Molha at ogt.com
Fri Dec 13 12:09:20 GMT 2013


Thanks Keiron

Yes , the 0 and 1 based systems already cause some confusion... and the fact that there is an inconsistency between the underlying database and presentation layer in USCS might be there to help but to me it only makes things worse :-)
 
Cheers

Duarte


-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Kieron Taylor
Sent: 13 December 2013 12:04
To: dev at ensembl.org
Subject: Re: [ensembl-dev] 1-based coordinate system Vs 0-based coordinate system

Hi Duarte,

Ensembl is uniformly 1-based. I refer you to UCSC's FAQ on their coordinate system, where their approach is explained well:

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1

They differentiate between database level and presentational level. I can only guess that their Blat server reports "presentation coordinates" 
instead of their true internal coordinates.

You need only be concerned with the UCSC internal coordinate system when you interact with specific file formats, or a UCSC database directly. 
Ensembl would be concerned if our website did NOT report the same sequence and coordinates as the UCSC web tools.

Regards,

--
Kieron Taylor PhD.
Ensembl Core team
EBI


On 13/12/2013 11:46, Duarte Molha wrote:
> Dear Developers
>
> I was wondering if you could give me a quick explanation on this.
>
> I am aware that ensembl uses 1-based coordinate system and UCSC uses
> 0-based...
>
> However... consider this sequence:
>
> ctaagccacaccataactgacttctaggcattcatctttcttccacttaaattcattctc
>
> When I blated this sequence, both UCSC and Ensembl blat servers gave be
> the exact same coordinate for the hit:
>
> chr14:79498951-79499010
>
> However I would expect, if I put this exact coordinates in ensembl
> browser and in UCSC genome browser the sequence retrieved would be
> trimmed by one base in ENSEMBL.
>
> However this is not the case. Can you explain me why this is?
>
> I am sure you probably have already explained this before so I apologize
> beforehand if this is a dumb question.
>
> Best regards
>
> Duarte
>
>
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