[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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