Gene Calling in Viruses

Gene Calling is a fancy way of saying "this region of DNA corresponds to a gene". This is usually done with computational models, using heuristics such as:

• open reading frames (ORFs)
• start / stop codons
• ribosome binding sites
• etc

Doing so in viruses is particularly tricky for many reasons, one of which is overlapping ORFs. For example, you might have a DNA strand:

AUG AAT AUG GAG ATG UGA UAA

AUG AAT AUG GAG ATG UGA
^^^                 ^^^
start               end 

**OR**

AUG AAT AUG GAG ATG UGA UAA
    ^^^                 ^^^
    start               end 

Both are valid ORFs, depending where transcription starts. Viruses pack a whole lot into their genome. They are very efficient.