[ensembl-dev] searchin on ensembl with perl API

[Giulietta Spudich]

> Hi Animesh,
>
> I believe you may have misunderstood my question or maybe I'm just not
> use the Ensembl API yet.
>
> If I understood it correctly, the code you send gets me all genes on a
> specific slice. What I want to do is emulate the search results on the
> ensebml site. For example, I go to http://www.ensembl.org/ enter the
> search 'histone h2a histone cluster 1' and get a list of 21 genes for
> human, 19 for mus musculus and several others for other organisms.
Hi Carnë ,

We don't usually recommend relying on Lucene searches that way, as the 
search engine looks for hits to the text you're entering, and they might 
not be related to your gene of interest.  Meaning, if you search for RHO 
you get rhodopsin-like proteins, and other genes with RHO in the name or 
description that are not related to Rhodopsin at all.  Also, you could 
miss genes that are homologous but have not been named in exactly the 
same way.  I see with your search that every hit is relevant to the 
histone h2a cluster, but are you missing genes in all species this way?

Depending what you're looking for, consider searching with the family ID 
or pull out all homologues of, for example, a human histone h2a hit.  
Here's what I mean on the website:

http://www.ensembl.org/Homo_sapiens/Gene/Family?g=ENSG00000164508;r=6:25726291-25726790;t=ENST00000297012

(Family ID is ENSFM00600000921125)

or orthologues:

http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=ENSG00000164508;r=6:25726291-25726790;t=ENST00000297012

The API tutorial explores both:

http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html

Hope that helps.

Giulietta

> What I need is that list of genes, just the IDs are fine.
>
> Carnë
>
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