coderet: How to match a protein sequence to its cds sequence?

Question

[Eliad]

I used coderet to extract the cds and protein sequences from a gbff file. The output sequences are indexed, but the numbers don't match between the two outputs. Therefore I can't match each protein sequence to its cds (nucleotide) sequence. How can I overcome this problem?

Answer 1

[Michael]

Try exonerate with model protein2genome?