[BioC] function for translation of ORFs

[hpages at fhcrc.org]

Hi Ana,

There is a translate() function in the seqinr package (CRAN)
that does this. It supports all kinds of genetic codes, not
only the standard code. It also supports IUPAC ambiguity
letters in the coding DNA.

I've just added a translate() function to the Biostrings too
(2.10.4 and 2.11.4).
The input here must be RNA (RNAString object) or coding DNA
(DNAString object). It's the responsability of the user to
make sure that s/he is using the coding DNA and not its reverse
complement.
You can mask the introns in the input sequence if you know
their locations (see ?translate for an example): this way
they will be excluded from the translation process.
Unlike seqinr::translate(), it only supports the standard
genetic code but other codes could be added if needed.

This will be available via biocLite() in the next 24 hours.

Please let me know if you have any question.

Cheers,
H.


Quoting Ana Conesa <aconesa at cipf.es>:

> Dear list,
>
> Can someone indicate a R function for translating an open reading frame
> into a protein sequence?
>
> Thanks
>
> Ana
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor