[R] How to import ENSEMBL text data using R

[Jean lobry]

Dear Anisah,

ENSEMBL data are at your hand under R:

>  library(seqinr)
>  choosebank("ensembl")
>  cat(banknameSocket$details, sep = "\n")
              ****     ACNUC Data Base Content      ****
Ensembl Release 47                       Last Updated: Dec 12, 2007
76,798,685,993 bases; 3,138,133 sequences; 8,132,077 subseqs; 0 refers.
  Tetraodon nigroviridis - Release 47_1i
  Oryzias latipes - Release 47_1c
  Homo sapiens - Release 47_36i
  Mus musculus - Release 47_37
  Rattus norvegicus - Release 47_34q
  Pan troglodytes - Release 47_21f
  Macaca mulatta - Release 47_10f
  Aedes aegypti - Release 47_1a
  Anopheles gambiae - Release 47_3i
  Bos taurus - Release 47_3d
  Caenorhabditis elegans - Release 47_180
  Canis familiaris - Release 47_2e
  Cavia porcellus - Release 47_1b
  Ciona intestinalis - Release 47_2g
  Ciona savignyi - Release 47_2e
  Dasypus novemcinctus - Release 47_1d
  Drosophila melanogaster - Release 47_43b
  Echinops telfairi - Release 47_1d
  Erinaceus europaeus - Release 47_1b
  Felis catus - Release 47_1b
  Gallus gallus - Release 47_2e
  Gasterosteus aculeatus - Release 47_1d
  Loxodonta africana - Release 47_1c
  Monodelphis domestica - Release 47_5b
  Myotis lucifugus - Release 47_1c
  Ornithorhynchus anatinus - Release 47_1d
  Oryctolagus cuniculus - Release 47_1d
  Otolemur garnettii - Release 47_1a
  Saccharomyces cerevisiae - Release 47_1g
  Sorex araneus - Release 47_1a
  Spermophilus tridecemlineatus - Release 47_1c
  Takifugu rubripes - Release 47_4g
  Tupaia belangeri - Release 47_1b
  Xenopus tropicalis - Release 47_41g

See the seqinr intro manual here:
http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf
to make queries and import sequence data.

Best,

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/