[ensembl-dev] species names

Stephen Fitzgerald stephenf at ebi.ac.uk
Wed Jun 27 11:57:41 BST 2012


Hi Jonathan, running this on the command line should give you the species 
names in compara-67, which you can then pipe in to grep for your species 
of interest.


mysql -uanonymous -hensembldb.ensembl.org -P5306 -Densembl_compara_67 
-e"select name from genome_db"
+-------------------------------+
| name                          |
+-------------------------------+
| ailuropoda_melanoleuca        |
| ancestral_sequences           |
| anolis_carolinensis           |
| bos_taurus                    |
| caenorhabditis_elegans        |
| callithrix_jacchus            |
| canis_familiaris              |
| cavia_porcellus               |
| choloepus_hoffmanni           |
| ciona_intestinalis            |
| ciona_savignyi                |
| danio_rerio                   |
| dasypus_novemcinctus          |
| dipodomys_ordii               |
| drosophila_melanogaster       |
| echinops_telfairi             |
| equus_caballus                |
| erinaceus_europaeus           |
| felis_catus                   |
| gadus_morhua                  |
| gallus_gallus                 |
| gasterosteus_aculeatus        |
| gorilla_gorilla               |
| homo_sapiens                  |
| latimeria_chalumnae           |
| loxodonta_africana            |
| macaca_mulatta                |
| macropus_eugenii              |
| meleagris_gallopavo           |
| microcebus_murinus            |
| monodelphis_domestica         |
| mus_musculus                  |
| myotis_lucifugus              |
| nomascus_leucogenys           |
| ochotona_princeps             |
| oreochromis_niloticus         |
| ornithorhynchus_anatinus      |
| oryctolagus_cuniculus         |
| oryzias_latipes               |
| otolemur_garnettii            |
| pan_troglodytes               |
| petromyzon_marinus            |
| pongo_abelii                  |
| procavia_capensis             |
| pteropus_vampyrus             |
| rattus_norvegicus             |
| saccharomyces_cerevisiae      |
| sarcophilus_harrisii          |
| sorex_araneus                 |
| spermophilus_tridecemlineatus |
| sus_scrofa                    |
| taeniopygia_guttata           |
| takifugu_rubripes             |
| tarsius_syrichta              |
| tetraodon_nigroviridis        |
| tupaia_belangeri              |
| tursiops_truncatus            |
| vicugna_pacos                 |
| xenopus_tropicalis            |
+-------------------------------+


On Wed, 27 Jun 2012, jonathan myles wrote:

> Hi
>
> Sorry, this is such an elementary one that I'm really  embarrassed
> that I can't find it in the documentation
>
> For a given species, eg mycosphaerella graminicola, how do I find the
> precise string which represents that species for querying the ENSEMBL
> or compara databases?
>
> Thank you
>
> Jonathan
>
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