[Bioc-sig-seq] Downloading a sequence from the NCBI

[Martin Morgan]

On 07/19/2010 03:04 PM, Ivan Gregoretti wrote:
> 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)

library(annotate)
getSEQ(getGI("AF441733.2"))

is one way.

Martin

> 
> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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