Once upon a time, Matthew Muller wrote:
> I was using org.biojava.bio.seq.genomic.TranslatedRegion to bind a protein sequence
> to it's mRNA sequence. I see that in BioJava 1.3, the whole package has been
> dropped.
>
> I want an object model that links mRNA, protein translations, and Features of both
> the mRNA and Protein.
>
> I'm guessing that the capability is still there but the classes are too abstract for
> me to understand. I suspect I need to use a FramedFeature. FramedFeatures implement
> the concept of a Translated Region but has no place for the Protein Sequence itself.
Ah, sorry about this. We got the impression that nobody was
using this package, and it wasn't being well-maintained. See:
http://biojava.org/pipermail/biojava-l/2002-November/003292.html
(there were no replies).
The `normal' thing to do if you want the protein sequence is
something like:
SymbolList prot = RNATools.translate(cdsFeature.getSymbols());
But I assume you're talking about associating protein sequences
which aren't always going to be 100% identical to the translation
of the RNA sequence. In this case, the best thing to do might
be to put the protein sequence as a property in the Annotation
object of the feature.
Or am I missing something here?
Does anyone else miss the seq.genomic package? Should we be
reinstating it?
Thomas.
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