[Biojava-l] TranslatedRegion

[Matthew Muller]

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.

Thanks!

Matthew Muller
Nuvelo
mullermw at nuvelo.com
tel: 408/215-4503
fax: 408/524-8129