[ensembl-dev] [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: Transcript variation alleles - Email found in subject - Email found in subject - Email found in subject

Oliver, Gavin gavin.oliver at almacgroup.com
Wed Feb 2 16:19:53 GMT 2011


Cool, thanks.

 

What determines the strand it goes on?

 

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 16:15
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: Re: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: [ensembl-dev]
Transcript variation alleles - Email found in subject - Email found in
subject - Email found in subject

 

variation_feature objects have a strand just like all features in
Ensembl - most are on the forward strand (as this makes our life
easier!) but many are also on the reverse strand.

 

As I mentioned earlier, you can check this using:

 

$vf->seq_region_strand

 

which will return a value of 1 (forward) or -1 (reverse).

On 2 February 2011 16:09, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

Ok...

 

So as it stands the alleles I am returning are genomic and called via
variation features.  Are they always relative to the forward strand?

 

 

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 16:04
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: [ensembl-dev] Transcript
variation alleles - Email found in subject - Email found in subject -
Email found in subject

 

Well yes, of course it depends on what you mean!

 

A transcript object in Ensembl represents the region of the genome that
generates the cDNA, not the mRNA itself - this is the only thing that
we'd be able to transfer the variation_feature object to, as I don't
think there is an Ensembl object representing the mRNA.

 

 


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