[Seqinr-forum] Retrieve Gene Sequence from Ensembl

[Jean lobry]

Dear all,

How can i get all the human gene sequence from Ensembl?

How can i get the sequence for a certain gene? e.g. 'ENSG00000141510'

Best Regards,

Rocky


Rocky,

Try this as a starter:

library(seqinr)
choosebank("ensembl")
query("all","T=CDS", virtual = TRUE)
all$nelem # 892572 CDS
query("list1","all AND K=ENSG00000141510")
list1$nelem # 3 sequences because of alternative splicing
myseqs <- getSequence(list1)
myprots <- getTrans(myseqs)
dotPlot(myprots[[1]], myprots[[2]])

See also chapter 6 "importing zlib-compressed sequences" for
an example with 78573 human CDS (not supported on windows).

Best,

Z.

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
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