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

[Javier Herrero]

Dear Zhang

The query/target naming has always been quite confusing in the pairwise 
alignment pipeline. When running an alignment, you use a sequence 
(query) to look for similar regions in another sequence (target genome). 
The pairwise alignment pipeline has three major steps: (a) raw 
alignments; (b) chaining; and (c) netting. The chaining step tries to 
link all the raw alignments that are in the same order and orientation 
to create a longer structure called chain. The netting step requires you 
to define a target genome such as the so-called nets are the subset of 
chains that form the best-in-genome alignment. In other words, the final 
set will provide you for each bp of the target genome with the best 
match on the other genome.

As I said earlier, query and target are often times confusing terms. To 
make the situation worse, we use to run the pipeline such as the query 
for the raw alignment step was the target for the chaining and netting 
steps and vice versa. We have now changed the way we refer to both 
sequences and call them reference and non-reference genomes. We find 
that nomenclature less confusing.

Kind regards

Javier

On 18/04/12 09:43, Dan Barrell wrote:
> Hi,
>
> 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 very out of date as we no longer build on low coverage genomes in 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:
>
> ensembl-compara/docs/README-low-coverage-genome-aligner
>
> Dan
>
>
>
>
>
>
>
>
>
> 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
>>
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org
>> List admin (including subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog:http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120418/0444abb2/attachment.html>