[BioC] import gene annotations from genbank
Hans-Rudolf Hotz
hrh at fmi.ch
Mon Jun 3 09:41:28 CEST 2013
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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
More information about the Bioconductor
mailing list