[ensembl-dev] RNA Edits

[Andy Yates]

Hi Trevor,

RNA edits are used in two major places in the Ensembl API. Firstly is in Transcripts where edits are applied to the RNA sequence where we find mis-matches in the spliced product we can change to create the correct sequence. In this case _rna_edit attributes are attached via transcript_attrib. The second case is in the SequenceAdaptor where edits are attached to a sequence region via seq_region_attrib. 

Edits are generated when there is a mis-match in the sequence between the contig an LRG is attached to & the reported LRG sequence. For example LRG_29 has a mismatch with the contig AC008863.8 at position 107678 (in the LRG) where we need a T. Edits are in sequence coordinates (counting from 1).

Hope this has helped to clear up any confusion,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 22 Mar 2012, at 17:54, PATERSON Trevor wrote:

> Hi
>  
> Is there any documentation to help me understand what is going on with the 'RNA Edits' that are cached on construction of a SequenceAdaptor in the PerlAPI?
>  
> The only doumentation that I can find  about RNA Edits is in an apparently out of date file on the ftp server... 
> ftp://ftp.ensembl.org/pub/ensembl/misc-scripts/attribute_types/attrib_type.txt
> which cryptically says for this attribute type: 
> # Drosophila. Sometimes sequences have been manually altered to remove one base, and this alters the whole translation
> 145	_rna_edit	rna_edit	RNA edit
> 
> Is there better documentation on the various attribute types somewhere?
> Also
> How are RNA Edits related to LRGs? ( are they LRGs? in humans they are on the same coordinate system...)
> Under what circumstances are sequences retrieved by the SequenceAdaptor 'RNA Editted' according to the cached information?
>  
> I am guessing that the RNA Edits are just an edge-case that have been levered in to the schema, I only became aware of them when I started looking into using LRGs.
>  
> Thanks
>  
> trevor
>  
>  
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
> 
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