[BioC] dumb question: using Biostrings (or something else) to translate DNA bases to amino acid codes

[Paul Shannon]

Hi Robert,

Your function works nicely.  Thank you!

  - Paul

On Jan 25, 2008, at 9:27 PM, Robert Gentleman wrote:

> for reasonably short sequences (like most genes)
>
> library(Biostrings)
>  DNA2AA = function(DNAseq) {
>     if(length(DNAseq) > 1 ) stop("only length one sequences, please")
>     nc = nchar(DNAseq)
>     Dtriples = substring(DNAseq, seq(1, nc, by=3), seq(3, nc, 3))
>     paste(GENETIC_CODE[Dtriples], collapse="")
>  }
>
>  will do it. The restriction to length one sequences is due to the  
> semantics of substring
>
>  best wishes
>    Robert
>
>
>
> lamon at fhcrc.org wrote:
>> Try the seqinr package.
>> Lynn
>> Quoting Paul Shannon <pshannon at systemsbiology.org>:
>>> I was so sure I could find this capability in Biostrings.  It may  
>>> be  there, or
>>> elsewhere, but lots of looking has not revealed it to me.  Is  
>>> there a  package
>>> which implements the genetic code?
>>>
>>> Sheepishly,
>>>
>>>   - Paul
>>>
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>
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org