[ensembl-dev] Details of the Marker_Feature / ePCR pipeline

[PATERSON Trevor]

I have some  questions about using Marker_Feature annotations  in Ensembl. We are thinking about cross referencing Markers from some of our data resources, giving us a link in from genetic maps to the Ensembl annotated genome. I can't find much detailed documentation about the creation and use of Marker_Features so would appreciate if anyone can give me some specific information.


 1.  I take it that for each genome build (or ensembl release?) the ePCR analysis of Marker primer pairs is done afresh - rather than mapping the previous marker coordinates to a new build? and that there is a cutoff threshold  to discard multiple mappings (map weight > 3?).
 2.  I had assumed that the Marker ePCR would be  performed on the assembled chromosome/toplevel assembly: but there is no entry 'marker.build = toplevel' in table 'meta' analagous to 'gene.build=toplevel'. Furthermore, it looks like (in the case of cows and humans where I have looked) a very small proportion of the markers are mapped on to the next level down (scaffold, supercontig or contig). Obviously these don't show up on the chromosomes - but can be found by searching by marker name and are displayed on the contig.
 3.  When I delve into the PerlAPI sourcecode it looks to me like marker features are always searched on the toplevel coordinate system, but also on other CS levels. Presumably this unpleasantness is because there is no use of a 'build' entry in table 'meta', and to catch any markers mapped to the supercontigs etc.
 4.  Which different resources of Markers are imported into Ensembl? Is this decided per species? Is UniSTS always imported for every species?
 5.  If we want add markers to the Ensembl pipeline, is the correct approach to add markers and maps to UniSTS database, and will these then be pulled automatically into future Ensembl release builds?

Thanks for any help...or pointers to more documentation.

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/

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