[BioC] biostrints translate() ambiguities?

James Walters [guest] guest at bioconductor.org
Thu Nov 24 19:57:36 CET 2011

Can someone please advise me on an efficient way to deal with translating coding sequence that contains ambiguities using Biostrings?  The Biostrings translate() function returns an error and I've not been able to find an obvious work-around.

I did find this exact question posted in March:


And while I think the suggestion of translating to 'X' is a satisfactory solution, there doesn't seem to have been any further action or advice offered on this front.  

Thank you , Jamie

> translate(DNAString("ATGGGGGCCTGTACC"))
  5-letter "AAString" instance
seq: MGACT
> translate(DNAString("ATGGGGGCCTGTACN"))
Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, skipcode,  : 
  not a base at pos 15

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biostrings_2.22.0 IRanges_1.12.1   

loaded via a namespace (and not attached):
[1] tools_2.14.0

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