[ensembl-dev] documentation missing

[Miguel Pignatelli]

Hi Joe,

On 12/02/13 16:02, Joe Carl wrote:
> I'm reading the compara database scheme webpage
> (http://www.ensembl.org/info/docs/api/compara/compara_schema.html), and
> noticed the three most intersting functions (to me) are missing.
>
> where is the documentation for the following
>
>   * species_tree_node
>     <http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_node>
>   * species_tree_node_tag
>     <http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_node_tag>
>   * species_tree_roo
>     <http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_root>t
>

Thanks for reporting this. I will make sure that the documentation for 
those tables are properly displayed in the next release.

Those tables contain the species tree used in the gene gain/loss 
analysis (http://www.ensembl.org/Help/View?id=379), i.e, they contain 
the full Ensembl species tree but in a ultrametric, binary format.

If I understand your problem correctly, you need to look at the 
gene_tree_node, gene_tree_root and homology (and perhaps 
homology_member) tables. Or better still, use the API to fetch the data.

Let us know if you need any help with this.

Cheers,

M;

>
> My goal is the following:
>
> 1) Grab the phylgentic trees already generated by ensemble (for specific
> Gene ID)
>       a) Newicks
>       b) Sequences by species
> 2) Grab the DN/DS for various branch points from Pig to Human
>
> If I need to I will grab the gene ID for each species and then determine
> the proper nucleotide sequence and grab those, using the newick
> calculate Dn/DS using PAML to get descendant predicted LCA sequences.
>
> Is there a better way to do this than I have outlined?
>
> Joe
>
>
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-- 

Miguel Pignatelli, PhD

Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
Room A3-33
Phone + 44 (0) 1223 494 598
Fax   + 44 (0) 1223 494 468