[BioC] import gene annotations from genbank

Sean [guest] guest at bioconductor.org
Sat Jun 1 01:19:14 CEST 2013

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.


 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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        

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