[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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