BiomaRt Arabidopsis genome unavailable
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oberlins ▴ 10
@oberlins-9307
Last seen 5.0 years ago
Switzerland

I wanted to retrieve sequences from the Arabidopsis thaliana genome via the biomArt package, but could no find it on the list of available datasets (see below). Is there any other way to retrieve the data?

> listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

> listDatasets(useMart("ENSEMBL_MART_ENSEMBL"))
                          dataset                                 description         version
1          oanatinus_gene_ensembl      Ornithorhynchus anatinus genes (OANA5)           OANA5
2         cporcellus_gene_ensembl             Cavia porcellus genes (cavPor3)         cavPor3
3         gaculeatus_gene_ensembl      Gasterosteus aculeatus genes (BROADS1)         BROADS1
4          lafricana_gene_ensembl          Loxodonta africana genes (loxAfr3)         loxAfr3
5  itridecemlineatus_gene_ensembl  Ictidomys tridecemlineatus genes (spetri2)         spetri2
6         choffmanni_gene_ensembl         Choloepus hoffmanni genes (choHof1)         choHof1
7          csavignyi_gene_ensembl              Ciona savignyi genes (CSAV2.0)         CSAV2.0
8             fcatus_gene_ensembl         Felis catus genes (Felis_catus_6.2) Felis_catus_6.2
9        rnorvegicus_gene_ensembl          Rattus norvegicus genes (Rnor_6.0)        Rnor_6.0
10         psinensis_gene_ensembl      Pelodiscus sinensis genes (PelSin_1.0)      PelSin_1.0
11          cjacchus_gene_ensembl   Callithrix jacchus genes (C_jacchus3.2.1)  C_jacchus3.2.1
12        ttruncatus_gene_ensembl          Tursiops truncatus genes (turTru1)         turTru1
13       scerevisiae_gene_ensembl    Saccharomyces cerevisiae genes (R64-1-1)         R64-1-1
14          celegans_gene_ensembl     Caenorhabditis elegans genes (WBcel235)        WBcel235
15          csabaeus_gene_ensembl       Chlorocebus sabaeus genes (ChlSab1.1)       ChlSab1.1
16        oniloticus_gene_ensembl     Oreochromis niloticus genes (Orenil1.0)       Orenil1.0
17         trubripes_gene_ensembl           Takifugu rubripes genes (FUGU4.0)         FUGU4.0
18        amexicanus_gene_ensembl        Astyanax mexicanus genes (AstMex102)       AstMex102
19          pmarinus_gene_ensembl     Petromyzon marinus genes (Pmarinus_7.0)    Pmarinus_7.0
20        eeuropaeus_gene_ensembl         Erinaceus europaeus genes (eriEur1)         eriEur1
21       falbicollis_gene_ensembl      Ficedula albicollis genes (FicAlb_1.4)      FicAlb_1.4
22      ptroglodytes_gene_ensembl          Pan troglodytes genes (CHIMP2.1.4)      CHIMP2.1.4
23         etelfairi_gene_ensembl            Echinops telfairi genes (TENREC)          TENREC
24     cintestinalis_gene_ensembl               Ciona intestinalis genes (KH)              KH
25       nleucogenys_gene_ensembl         Nomascus leucogenys genes (Nleu1.0)         Nleu1.0
26           sscrofa_gene_ensembl              Sus scrofa genes (Sscrofa10.2)     Sscrofa10.2
27        ocuniculus_gene_ensembl     Oryctolagus cuniculus genes (OryCun2.0)       OryCun2.0
28     dnovemcinctus_gene_ensembl      Dasypus novemcinctus genes (Dasnov3.0)       Dasnov3.0
29         pcapensis_gene_ensembl           Procavia capensis genes (proCap1)         proCap1
30          tguttata_gene_ensembl     Taeniopygia guttata genes (taeGut3.2.4)     taeGut3.2.4
31        mlucifugus_gene_ensembl            Myotis lucifugus genes (myoLuc2)         myoLuc2
32          hsapiens_gene_ensembl              Homo sapiens genes (GRCh38.p3)       GRCh38.p3
33          pformosa_gene_ensembl       Poecilia formosa genes (PoeFor_5.1.2)    PoeFor_5.1.2
34             mfuro_gene_ensembl  Mustela putorius furo genes (MusPutFur1.0)    MusPutFur1.0
35        tbelangeri_gene_ensembl            Tupaia belangeri genes (tupBel1)         tupBel1
36           ggallus_gene_ensembl               Gallus gallus genes (Galgal4)         Galgal4
37       xtropicalis_gene_ensembl           Xenopus tropicalis genes (JGI4.2)          JGI4.2
38         ecaballus_gene_ensembl              Equus caballus genes (EquCab2)         EquCab2
39           pabelii_gene_ensembl                  Pongo abelii genes (PPYG2)           PPYG2
40        xmaculatus_gene_ensembl   Xiphophorus maculatus genes (Xipmac4.4.2)     Xipmac4.4.2
41            drerio_gene_ensembl                  Danio rerio genes (GRCz10)          GRCz10
42        lchalumnae_gene_ensembl         Latimeria chalumnae genes (LatCha1)         LatCha1
43     tnigroviridis_gene_ensembl Tetraodon nigroviridis genes (TETRAODON8.0)    TETRAODON8.0
44      amelanoleuca_gene_ensembl      Ailuropoda melanoleuca genes (ailMel1)         ailMel1
45          mmulatta_gene_ensembl               Macaca mulatta genes (MMUL_1)          MMUL_1
46         pvampyrus_gene_ensembl           Pteropus vampyrus genes (pteVam1)         pteVam1
47           panubis_gene_ensembl              Papio anubis genes (PapAnu2.0)       PapAnu2.0
48        mdomestica_gene_ensembl       Monodelphis domestica genes (monDom5)         monDom5
49     acarolinensis_gene_ensembl       Anolis carolinensis genes (AnoCar2.0)       AnoCar2.0
50            vpacos_gene_ensembl               Vicugna pacos genes (vicPac1)         vicPac1
51         tsyrichta_gene_ensembl            Tarsius syrichta genes (tarSyr1)         tarSyr1
52        ogarnettii_gene_ensembl          Otolemur garnettii genes (OtoGar3)         OtoGar3
53     dmelanogaster_gene_ensembl       Drosophila melanogaster genes (BDGP6)           BDGP6
54          mmurinus_gene_ensembl          Microcebus murinus genes (micMur1)         micMur1
55         loculatus_gene_ensembl        Lepisosteus oculatus genes (LepOcu1)         LepOcu1
56          olatipes_gene_ensembl                Oryzias latipes genes (HdrR)            HdrR
57          ggorilla_gene_ensembl           Gorilla gorilla genes (gorGor3.1)       gorGor3.1
58         oprinceps_gene_ensembl         Ochotona princeps genes (OchPri2.0)       OchPri2.0
59            dordii_gene_ensembl             Dipodomys ordii genes (dipOrd1)         dipOrd1
60            oaries_gene_ensembl                 Ovis aries genes (Oar_v3.1)        Oar_v3.1
61         mmusculus_gene_ensembl              Mus musculus genes (GRCm38.p4)       GRCm38.p4
62        mgallopavo_gene_ensembl            Meleagris gallopavo genes (UMD2)            UMD2
63           gmorhua_gene_ensembl                Gadus morhua genes (gadMor1)         gadMor1
64    aplatyrhynchos_gene_ensembl     Anas platyrhynchos genes (BGI_duck_1.0)    BGI_duck_1.0
65          saraneus_gene_ensembl               Sorex araneus genes (sorAra1)         sorAra1
66         sharrisii_gene_ensembl       Sarcophilus harrisii genes (DEVIL7.0)        DEVIL7.0
67          meugenii_gene_ensembl           Macropus eugenii genes (Meug_1.0)        Meug_1.0
68           btaurus_gene_ensembl                   Bos taurus genes (UMD3.1)          UMD3.1
69       cfamiliaris_gene_ensembl          Canis familiaris genes (CanFam3.1)       CanFam3.1

 

 

 

 

biomart retrive sequence • 2.7k views
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Thanks!

This works perfect.

 

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Entering edit mode
Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 12 weeks ago
United Kingdom

 

Hello,

The ensembl.org website only contain vertebrates species, to access plants genomes you will have to query the following sister website: http://plants.ensembl.org/index.html

> listMarts(host="plants.ensembl.org")
            biomart              version
1       plants_mart           Plant Mart
2 plants_variations Plant Variation Mart

> listDatasets(useMart(biomart="plants_mart",host="plants.ensembl.org"))
                   dataset                                                                 description
1        atauschii_eg_gene                          Aegilops tauschii genes (ASM34733v1 (2013-12-BGI))
2     obrachyantha_eg_gene                 Oryza brachyantha genes (Oryza_brachyantha.v1.4b (OGEv1.4))
3         ppersica_eg_gene                                   Prunus persica genes (Prupe1_0 (2013-03))
4     ptrichocarpa_eg_gene                            Populus trichocarpa genes (JGI2.0 (2010-01-JGI))
5       stuberosum_eg_gene                           Solanum tuberosum genes (SolTub_3.0 (SolTub_3.0))
6         sitalica_eg_gene                                   Setaria italica genes (JGIv2.0 (JGIv2.1))
7    slycopersicum_eg_gene Solanum lycopersicum str. Heinz 1706 genes (SL2.50 (2014-10-EnsemblPlants))
8          onivara_eg_gene                                 Oryza nivara genes (AWHD00000000 (2013-09))
9          ppatens_eg_gene                   Physcomitrella patens genes (ASM242v1 (2011-03-Phypa1.6))
10            gmax_eg_gene                                    Glycine max genes (V1.0 (JGI-Glyma-1.1))
11        sbicolor_eg_gene                                Sorghum bicolor genes (Sorbi1 (2007-12-JGI))
12       lperrieri_eg_gene                           Leersia perrieri genes (Lperr_V1.4 (2013-09-OGE))
13     bdistachyon_eg_gene                    Brachypodium distachyon genes (v1.0 (2010-02-Brachy1.2))
14       opunctata_eg_gene                               Oryza punctata genes (AVCL00000000 (2013-09))
15         oindica_eg_gene                          Oryza sativa Indica genes (ASM465v1 (2010-07-BGI))
16 smoellendorffii_eg_gene                       Selaginella moellendorffii genes (v1.0 (2011-05-ENA))
17   oglumaepatula_eg_gene                           Oryza glumaepatula genes (ALNU02000000 (2013-09))
18        obarthii_eg_gene                              Oryza barthii genes (Obart_v1.0 (2014-05-OGE))
19         osativa_eg_gene                         Oryza sativa Japonica genes (IRGSP-1.0 (IRGSP-1.0))
20    olucimarinus_eg_gene          Ostreococcus lucimarinus genes (ASM9206v1 (2011-01-EnsemblPlants))
21        hvulgare_eg_gene                                 Hordeum vulgare genes (082214v1 (IBSC_1.0))
22       boleracea_eg_gene                                       Brassica oleracea genes (v2.1 (v2.1))
23   omeridionalis_eg_gene          Oryza meridionalis genes (Oryza_meridionalis_v1.3 (2014-10-MAKER))
24         alyrata_eg_gene                         Arabidopsis lyrata genes (v.1.0 (2008-12-Araly1.0))
25      orufipogon_eg_gene                             Oryza rufipogon genes (PRJEB4137 (2013-09-OGE))
26       taestivum_eg_gene                             Triticum aestivum genes (IWGSC1.0+popseq (2.2))
27           brapa_eg_gene                       Brassica rapa genes (IVFCAASv1 (bra_v1.01_SP2010_01))
28       vvinifera_eg_gene                             Vitis vinifera genes (IGGP_12x (2012-07-CRIBI))
29           zmays_eg_gene                                                 Zea mays genes (AGPv3 (5b))
30     mtruncatula_eg_gene   Medicago truncatula str. A17 genes (MedtrA17_4.0 (2014-06-EnsemblPlants))
31     atrichopoda_eg_gene                          Amborella trichopoda genes (AMTR1.0 (2014-01-AGD))
32    creinhardtii_eg_gene                        Chlamydomonas reinhardtii genes (v3.1 (2007-11-ENA))
33 olongistaminata_eg_gene                  Oryza longistaminata genes (v0117-2013Aug (2013-09-Maker))
34        cmerolae_eg_gene                     Cyanidioschyzon merolae genes (ASM9120v1 (2008-11-ENA))
35     oglaberrima_eg_gene                               Oryza glaberrima genes (AGI1.1 (2011-05-AGI))
36          tcacao_eg_gene    Theobroma cacao genes (Theobroma_cacao_20110822 (2014-05-EnsemblPlants))
37      macuminata_eg_gene                                  Musa acuminata genes (MA1 (2012-08-Cirad))
38         turartu_eg_gene                            Triticum urartu genes (ASM34745v1 (2013-04-BGI))
39       athaliana_eg_gene                        Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10))
                                            version
1                          ASM34733v1 (2013-12-BGI)
2                 Oryza_brachyantha.v1.4b (OGEv1.4)
3                                Prupe1_0 (2013-03)
4                              JGI2.0 (2010-01-JGI)
5                           SolTub_3.0 (SolTub_3.0)
6                                 JGIv2.0 (JGIv2.1)
7                    SL2.50 (2014-10-EnsemblPlants)
8                            AWHD00000000 (2013-09)
9                       ASM242v1 (2011-03-Phypa1.6)
10                             V1.0 (JGI-Glyma-1.1)
11                             Sorbi1 (2007-12-JGI)
12                         Lperr_V1.4 (2013-09-OGE)
13                         v1.0 (2010-02-Brachy1.2)
14                           AVCL00000000 (2013-09)
15                           ASM465v1 (2010-07-BGI)
16                               v1.0 (2011-05-ENA)
17                           ALNU02000000 (2013-09)
18                         Obart_v1.0 (2014-05-OGE)
19                            IRGSP-1.0 (IRGSP-1.0)
20                ASM9206v1 (2011-01-EnsemblPlants)
21                              082214v1 (IBSC_1.0)
22                                      v2.1 (v2.1)
23          Oryza_meridionalis_v1.3 (2014-10-MAKER)
24                         v.1.0 (2008-12-Araly1.0)
25                          PRJEB4137 (2013-09-OGE)
26                            IWGSC1.0+popseq (2.2)
27                  IVFCAASv1 (bra_v1.01_SP2010_01)
28                         IGGP_12x (2012-07-CRIBI)
29                                       AGPv3 (5b)
30             MedtrA17_4.0 (2014-06-EnsemblPlants)
31                            AMTR1.0 (2014-01-AGD)
32                               v3.1 (2007-11-ENA)
33                    v0117-2013Aug (2013-09-Maker)
34                          ASM9120v1 (2008-11-ENA)
35                             AGI1.1 (2011-05-AGI)
36 Theobroma_cacao_20110822 (2014-05-EnsemblPlants)
37                              MA1 (2012-08-Cirad)
38                         ASM34745v1 (2013-04-BGI)
39                          TAIR10 (2010-09-TAIR10)

Hope this helps,

Regards,

Thomas

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