Hi
Jonathan <div><br></div><div>species name and abbreviation also can find in public-plugins/ensembl/conf/SiteDefs.pm </div><div><br></div><div>Best</div><div><br></div><div>Gang Chen</div><div><br><div class="gmail_quote">
2012/6/27 <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
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1. species names (jonathan myles)<br>
2. Re: species names (Stephen Fitzgerald)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 27 Jun 2012 11:41:13 +0100<br>
From: jonathan myles <<a href="mailto:jonathanmyles1@googlemail.com">jonathanmyles1@googlemail.com</a>><br>
Subject: [ensembl-dev] species names<br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
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<br>
Hi<br>
<br>
Sorry, this is such an elementary one that I'm really embarrassed<br>
that I can't find it in the documentation<br>
<br>
For a given species, eg mycosphaerella graminicola, how do I find the<br>
precise string which represents that species for querying the ENSEMBL<br>
or compara databases?<br>
<br>
Thank you<br>
<br>
Jonathan<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 27 Jun 2012 11:57:41 +0100 (BST)<br>
From: Stephen Fitzgerald <<a href="mailto:stephenf@ebi.ac.uk">stephenf@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] species names<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:alpine.LRH.2.00.1206271150540.16190@login-r6-1.ebi.ac.uk">alpine.LRH.2.00.1206271150540.16190@login-r6-1.ebi.ac.uk</a>><br>
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<br>
Hi Jonathan, running this on the command line should give you the species<br>
names in compara-67, which you can then pipe in to grep for your species<br>
of interest.<br>
<br>
<br>
mysql -uanonymous -<a href="http://hensembldb.ensembl.org" target="_blank">hensembldb.ensembl.org</a> -P5306 -Densembl_compara_67<br>
-e"select name from genome_db"<br>
+-------------------------------+<br>
| name |<br>
+-------------------------------+<br>
| ailuropoda_melanoleuca |<br>
| ancestral_sequences |<br>
| anolis_carolinensis |<br>
| bos_taurus |<br>
| caenorhabditis_elegans |<br>
| callithrix_jacchus |<br>
| canis_familiaris |<br>
| cavia_porcellus |<br>
| choloepus_hoffmanni |<br>
| ciona_intestinalis |<br>
| ciona_savignyi |<br>
| danio_rerio |<br>
| dasypus_novemcinctus |<br>
| dipodomys_ordii |<br>
| drosophila_melanogaster |<br>
| echinops_telfairi |<br>
| equus_caballus |<br>
| erinaceus_europaeus |<br>
| felis_catus |<br>
| gadus_morhua |<br>
| gallus_gallus |<br>
| gasterosteus_aculeatus |<br>
| gorilla_gorilla |<br>
| homo_sapiens |<br>
| latimeria_chalumnae |<br>
| loxodonta_africana |<br>
| macaca_mulatta |<br>
| macropus_eugenii |<br>
| meleagris_gallopavo |<br>
| microcebus_murinus |<br>
| monodelphis_domestica |<br>
| mus_musculus |<br>
| myotis_lucifugus |<br>
| nomascus_leucogenys |<br>
| ochotona_princeps |<br>
| oreochromis_niloticus |<br>
| ornithorhynchus_anatinus |<br>
| oryctolagus_cuniculus |<br>
| oryzias_latipes |<br>
| otolemur_garnettii |<br>
| pan_troglodytes |<br>
| petromyzon_marinus |<br>
| pongo_abelii |<br>
| procavia_capensis |<br>
| pteropus_vampyrus |<br>
| rattus_norvegicus |<br>
| saccharomyces_cerevisiae |<br>
| sarcophilus_harrisii |<br>
| sorex_araneus |<br>
| spermophilus_tridecemlineatus |<br>
| sus_scrofa |<br>
| taeniopygia_guttata |<br>
| takifugu_rubripes |<br>
| tarsius_syrichta |<br>
| tetraodon_nigroviridis |<br>
| tupaia_belangeri |<br>
| tursiops_truncatus |<br>
| vicugna_pacos |<br>
| xenopus_tropicalis |<br>
+-------------------------------+<br>
<br>
<br>
On Wed, 27 Jun 2012, jonathan myles wrote:<br>
<br>
> Hi<br>
><br>
> Sorry, this is such an elementary one that I'm really embarrassed<br>
> that I can't find it in the documentation<br>
><br>
> For a given species, eg mycosphaerella graminicola, how do I find the<br>
> precise string which represents that species for querying the ENSEMBL<br>
> or compara databases?<br>
><br>
> Thank you<br>
><br>
> Jonathan<br>
><br>
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><br>
<br>
<br>
<br>
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End of Dev Digest, Vol 24, Issue 45<br>
***********************************<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><font face="verdana, sans-serif" size="1">Gang Chen</font></div><div><font face="verdana, sans-serif" size="1">TILSI</font></div><div><font face="verdana, sans-serif" size="1"><span style="background-color:rgb(255,255,255)">Taicang Institute For Life Science Information</span><br style="background-color:rgb(255,255,255)">
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