[ensembl-dev] RNA Edits

[PATERSON Trevor]

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The only doumentation that I can find  about RNA Edits is in an apparently out of date file on the ftp server...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<mailto: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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120322/949d6c96/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120322/949d6c96/attachment.ksh>