[Bioc-sig-seq] Downloading a sequence from the NCBI
Ivan Gregoretti
ivangreg at gmail.com
Tue Jul 20 00:04:28 CEST 2010
How do I download the GeneBank record AF441733.2?
(Mus musculus clone RP23-225M6 45S pre-ribosomal RNA gene, partial
sequence; and intergenic spacer, partial sequence)
I know that I could manually download it as a fasta file and then read
it into R but there is probably a single step strategy.
I wanted to use biomaRt but since the record seems to be absent from
Ensembl, I can't expect biomaRt to fetch it. Can I?
Thank you,
Ivan
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.4.0
loaded via a namespace (and not attached):
[1] RCurl_1.4-2 XML_3.1-0
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