How to verify ORF Finder results

Question

[bondcarbond]

Hi all,

I sequenced the complete mitochondrial genome of a species and i annotated it using MITOS. Then i used ORF Finder to verify MITOS Annotation. My question is how to verify if ORF Finder prediction is right, because if i look at the sequence i can find start-stop codons before and after ORF Finder prediction.. I thought maybe to performe an alignment with other mt genomes from close related species and make comparisons, but is there another way? maybe some accurate method that im not aware of?

thanks for the help!

Answer 1

[Michael]

ORF finding is exact, if implemented correctly, also the correct genetic code must be used. If you don't trust the ORFs you can use getOrf with a mitochondrial code for this or a related taxon and compare the result. That there are more start and stop codons is normal, they are maybe just not in frame. Also, an ORF finding does not really do much to validate a gene prediction, because the minimal requirement for a gene would be the presence of an ORF.