[Biojava-l] TranslatedRegion

[Thomas Down]

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.