[ensembl-dev] Confused by the target/query core database in whole genome alignment based gene build

Dan Barrell db8 at sanger.ac.uk
Wed Apr 18 09:43:21 BST 2012


The document low_coverage_gene_build.txt is quite old and possibly very 
out of date as we no longer build on low coverage genomes in Ensembl. As 
far as I know, the reason that the semantics of the reference and target 
terms got swapped is to do with the importance of directionality in a 
Net. When dealing with the low coverage genomes the idea was that they 
wanted the species they were projecting onto as the reference because it 
is important that each bp in the target species aligns to at most one 
location in the reference species.

I would suggest you also look at the Ensembl Compara documentation which 
is maintained here:



On 17/04/12 12:47, Zhang Di wrote:
> Hi,
> I'm using ensembl pipeline for projection genebuild.
> when I read the doc low_coverage_gene_build.txt, I was confused by the 
> target/query genome terms.
> It calls our newly sequenced genome the target, calls the reference 
> genome the query.
> It is contrary to lastz terms where target means reference and query 
> means our sequences.
> It just OK if I stick to this convention.
> However,
> In the whole genome alignment section in the same doc,
> It says that :
>     "each bp in the target genome should be represented at most once."
> What does it mean by saying "target"?
> lastz-chain-net produces the lastz termed "target genome" with this 
> property.
> Does it mean that I should set my genome as the reference genome, 
> while the genome from ensembl such as "human" as the non-reference in 
> the compara/hive pipeline?
> I can project human genes to my genome with this somewhat weird 
> setting, in the next wga2genes step?
> Some slice of human genome containing genes may exist several times in 
> the compara_db, how can it produce gene projection right here?
> Thanks
> Best Reguards
> -- 
> Zhang Di
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