Ensembl orthologue help

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goodyearkl
goodyearkl's picture
Ensembl orthologue help

Hi, I am new at using EMBL and I need to find orthologues between the genes of chromosome 7 of Saccharomyces cerevisiae and humans. I have a feeling it can be done with Ensembl, but I am not quite sure how to go about doing it. I am looking to find the % identities for class. I am very comfortable with NCBI but EBI is completely new to me.

Here is the exact question:

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font-family:"Times New Roman","serif"">Write down the steps you would follow to download all the Baker's yeast genes in chromosome VII with a Human Orthologous. In your results include Ensemb Gene ID, Description, Human Ensembl Gene ID, % Identity, and Human % Identity. Save your results in TSV (Tab Separated Values) format and submit them as part of your assignment.

Thanks again for any pointers!

I found this: http://www.ensembl.org/Saccharomyces_cerevisiae/Location/Chromosome?r=VII:860047-960047
but it is about as far as I managed.

Giulietta (Ense...
Giulietta (Ensembl Helpdesk)'s picture
Hi!

Hi!

You can do this with BioMart.  A short tutorial video is worth looking at here:

http://www.ensembl.org/Help/Movie?id=189

Basically, your database and dataset will be Ensembl genes, and Saccharomyces cerevisiae.    Filters will be 'chromosome 7' and attributes will be the homologues page, yeast orthologs.

There are ways to do this with the browser, but BioMart is more straighforward when considering a whole chromosome.  You can find it here: 
http://www.ensembl.org/biomart/martview

Questions like these are welcome at the Ensembl Helpdesk (helpdesk@ensembl.org)