[ensembl-dev] RNA Edits

[Andy Yates]

Hi Trevor

Yes it is an overloading of an already existing editing structure to provide the correct lrg sequence. The edit is only applied to the lrg sequence returned and not to the chromosome attached to the same contig.

Regards,

Andy

Sent from my mobile.

On 26 Mar 2012, at 10:45, PATERSON Trevor <trevor.paterson at roslin.ed.ac.uk> wrote:

> Hi 
> 
> thanks to all for the info 
> 
> The 'normal' use of rna_edit is clear...
> 
> And the use of rna_edit on the SequenceAdaptor for LRGs is a (cough) hack to create the sequence of the LRG?
> 
> Does this mean that every time you get back the sequence of an assembled chromosome slice that has an rna_edit for the LRG, 
> it is the editted sequence that you get back for the chromosome - or is it only when you specifically retrieve
> the LRG sequence you get back the editted sequence?
> 
> Cheers
> 
> trevor
> 
> 
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
> 
> Bioinformatics 
> The Roslin Institute
> Royal (Dick) School of Veterinary Studies
> University of Edinburgh
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> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andy Yates
> Sent: 23 March 2012 09:57
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] RNA Edits
> 
> 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
>> 
>> Bioinformatics
>> The Roslin Institute
>> Royal (Dick) School of Veterinary Studies University of Edinburgh 
>> Easter Bush Midlothian
>> EH25 9RG
>> Scotland UK
>> 
>> phone +44 (0)131 651 9157
>> 
>> http://bioinformatics.roslin.ed.ac.uk/
>> 
>> Please consider the environment before printing this e-mail
>> 
>> The University of Edinburgh is a charitable body, registered in 
>> Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
>> 
>> 
>> The University of Edinburgh is a charitable body, registered in 
>> Scotland, with registration number SC005336.
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