[ensembl-dev] Dev Digest, Vol 24, Issue 45

陈岗 danielchen06 at gmail.com
Wed Jun 27 13:14:25 BST 2012


Hi  Jonathan

species name and abbreviation also can find
in public-plugins/ensembl/conf/SiteDefs.pm

Best

Gang Chen

2012/6/27 <dev-request at ensembl.org>

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> Today's Topics:
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>   1. species names (jonathan myles)
>   2. Re: species names (Stephen Fitzgerald)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Jun 2012 11:41:13 +0100
> From: jonathan myles <jonathanmyles1 at googlemail.com>
> Subject: [ensembl-dev] species names
> To: dev at ensembl.org
> Message-ID:
>        <CAOXpw8LrWynbqB7du6gPH2h-9Gp41v2c0PfsQ2hLdTUirvZ9-g at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Jun 2012 11:57:41 +0100 (BST)
> From: Stephen Fitzgerald <stephenf at ebi.ac.uk>
> Subject: Re: [ensembl-dev] species names
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <alpine.LRH.2.00.1206271150540.16190 at login-r6-1.ebi.ac.uk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> 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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> >
>
>
>
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> End of Dev Digest, Vol 24, Issue 45
> ***********************************
>



-- 
Gang Chen
TILSI
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
P.R.China
Phone:(+86)512-82782588
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