How to translate HIV-1 gag-pol sequences?

Question

[andres.becerra]

I get HIV-1 sequences for polyprotein Gag-Pol from: http://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

And I need to translate them.

The problem is that the gag-pol region has a frameshift, and I don't know how to do the translation.

For example, If I get the sequence for reference genome K03455.1: http://www.ncbi.nlm.nih.gov/nuccore/K03455

I know there is a frameshift marked by the sequence tttttta. But how to translate gag-pol with the premature stop codons in the region?

[Devon Ryan]

Why not make life easy and just use the uniprot sequence? The tttttta sequence is making a pseudo-knot, so you'd otherwise need to visualize the structure to see what the translational machinery is actually translating.