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editing static content for 114 #848

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for genebuild content:

addign some new pages, editing others, and updating the strains page for rodents

We havent changed anything from the comparative analysis section on the mouse strains file, and we'd like to check with compara if that's still current and ok, so mentioning here @ens-sb and @twalsh-ebi so that they can offer their view on the topic.

I'd like to also wait for them to approve to merge anything, unless time is of the esence.

addign some new pages, editing others, and updating the strains page for
rodents
@twalsh-ebi
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Hi @EreboPSilva .. I think the text on comparative data in Mus_musculus_strains.inc is in need of an update.

Any thoughts (@EreboPSilva and @kamaldodiya) on whether it would be better to suggest a change in this PR or submit a separate pull request?

Comment on lines 15 to 17
<p>We generated a multiple genome alignment of all the genomes from the The Mouse Genomes Project with <i>Mus musculus</i>, <i>Rattus norvegicus</i> and additional four Mus species using our EPO pipeline. Additionally, we have computed a LastZ alignment of <i>Mus musculus</i> and <i>Mus spretus</i>.</p>

<p>We provide two sets of gene-trees and orthologues in Ensembl. The standard gene-trees and orthologues comprise genes from one representative for every Ensembl species, whilst the Murinae-specific gene-trees and orthologues comprise genes from all mouse strains and include genes from <i>Mus musculus</i>, <i>Mus spretus</i> and <i>Rattus norvegicus</i>. A stepwise approach via one these three species is required in order to compare genes from mouse strains to genes from species not in the Murinae set.</p>
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@twalsh-ebi twalsh-ebi Jan 6, 2025

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A suggestion it is. Now it's my turn to ask @EreboPSilva and @ens-sb to check if the updated text tallies with your understanding.

Suggested change
<p>We generated a multiple genome alignment of all the genomes from the The Mouse Genomes Project with <i>Mus musculus</i>, <i>Rattus norvegicus</i> and additional four Mus species using our EPO pipeline. Additionally, we have computed a LastZ alignment of <i>Mus musculus</i> and <i>Mus spretus</i>.</p>
<p>We provide two sets of gene-trees and orthologues in Ensembl. The standard gene-trees and orthologues comprise genes from one representative for every Ensembl species, whilst the Murinae-specific gene-trees and orthologues comprise genes from all mouse strains and include genes from <i>Mus musculus</i>, <i>Mus spretus</i> and <i>Rattus norvegicus</i>. A stepwise approach via one these three species is required in order to compare genes from mouse strains to genes from species not in the Murinae set.</p>
<p>Using our EPO pipeline, we generated a multiple genome alignment of 16 of the
reference-quality genomes from the The Mouse Genomes Project with <i>Mus
musculus</i>, <i>Rattus norvegicus</i> and an additional three <i>Mus</i>
species&colon; <i>Mus caroli</i>, <i>Mus pahari</i> and <i>Mus
spicilegus</i>. Additionally, we have computed a LastZ alignment of <i>Mus
spretus</i> and the three additional <i>Mus</i> species against the <i>Mus
musculus</i> reference genome.</p>
<p>We provide multiple sets of gene-trees and orthologues in Ensembl, two of
which include genes from a mouse genome. The standard gene-trees and
orthologues comprise genes from representatives of selected Ensembl species,
whilst the Murinae-specific gene-trees and orthologues comprise genes from
all mouse strains and include genes from <i>Mus musculus</i>, <i>Rattus
norvegicus</i>, <i>Mus spretus</i> and the three aforementioned <i>Mus</i>
species. A stepwise approach via one of these six species is required in
order to compare genes from mouse strains to genes from species not in the
Murinae set.</p>

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Thanks @twalsh-ebi ! Looks good to me!

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3 participants