[BioC] import gene annotations from genbank

[Hans-Rudolf Hotz]

Hi Sean


Have you looked at: "genoPlotR"
(http://genoplotr.r-forge.r-project.org/index.php)

Although, it has been primarily developed to plot genes and genome maps. 
It allows you to parse Genbank files.


Hans-Rudolf



On 06/01/2013 01:19 AM, Sean [guest] wrote:
>
> I am trying to find a way to conveniently load the genbank sequence annotations for a reference gene as a GRanges object.
>
> Specifically, I want to use the revised Cambridge reference sequence for human mitochondrial DNA, accession NC_012920.1. It seems like there ought to be a way to easily download the sequence and all of the genbank feature information as DNAStringSet and GRanges objects respectively.
>
> Thanks,
> Sean
>
>   -- output of sessionInfo():
>
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.26.1
>   [3] VariantTools_1.0.1                 VariantAnnotation_1.4.12
>   [5] BiocInstaller_1.8.3                ShortRead_1.16.4
>   [7] latticeExtra_0.6-24                RColorBrewer_1.0-5
>   [9] Rsamtools_1.10.2                   lattice_0.20-13
> [11] Biostrings_2.26.3                  GenomicRanges_1.10.7
> [13] IRanges_1.16.6                     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.6   Biobase_2.18.0         biomaRt_2.14.0
>   [4] bitops_1.0-5           DBI_0.2-5              GenomicFeatures_1.10.2
>   [7] gmapR_1.0.0            grid_2.15.3            hwriter_1.3
> [10] parallel_2.15.3        RCurl_1.95-4.1         RSQLite_0.11.2
> [13] rtracklayer_1.18.2     stats4_2.15.3          tools_2.15.3
> [16] XML_3.95-0.2           zlibbioc_1.4.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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