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Dear Zhang<br>
<br>
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.<br>
<br>
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.<br>
<br>
Kind regards<br>
<br>
Javier<br>
<br>
On 18/04/12 09:43, Dan Barrell wrote:
<blockquote cite="mid:4F8E7EA9.1080701@sanger.ac.uk" type="cite">
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Hi,<br>
<br>
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very out of date as we no longer build on low coverage genomes in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. <br>
<br>
I would suggest you also look at the Ensembl Compara documentation
which is maintained here:<br>
<br>
ensembl-compara/docs/README-low-coverage-genome-aligner<br>
<br>
Dan<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 17/04/12 12:47, Zhang Di wrote:
<blockquote
cite="mid:CAMHeD-eXYuTGRu46M2Hb=VhYufJWPiUmgNev=m7vtVn6ZhjDaA@mail.gmail.com"
type="cite">Hi,
<div><br>
</div>
<div>I'm using ensembl pipeline for projection genebuild.</div>
<div><br>
</div>
<div>when I read the doc low_coverage_gene_build.txt, I was
confused by the target/query genome terms.</div>
<div><br>
</div>
<div>It calls our newly sequenced genome the target, calls the
reference genome the query.</div>
<div><br>
</div>
<div>It is contrary to lastz terms where target means reference
and query means our sequences.</div>
<div><br>
</div>
<div>It just OK if I stick to this convention.</div>
<div><br>
</div>
<div>However,</div>
<div><br>
</div>
<div>In the whole genome alignment section in the same doc,</div>
<div><br>
</div>
<div>It says that :</div>
<div><br>
</div>
<div> "each bp in the target genome should be represented at
most once."</div>
<div><br>
</div>
<div>What does it mean by saying "target"?</div>
<div><br>
</div>
<div>lastz-chain-net produces the lastz termed "target genome"
with this property.</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>I can project human genes to my genome with this somewhat
weird setting, in the next wga2genes step?</div>
<div><br>
</div>
<div>Some slice of human genome containing genes may exist
several times in the compara_db, how can it produce gene
projection right here?</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Best Reguards</div>
<div><br>
</div>
<div>-- <br>
Zhang Di<br>
</div>
<br>
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<br>
<br>
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<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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