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.

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 >