I'm curious how FragGeneScan finds open reading frames. The three ways I could think of are below...does anybody know which one it is?
A) find the coding sequence only (e.g. ATG-xxx-xxx-STOP);
B) find a segment of the coding sequence only (e.g. ATG-xxx-xx or xxx-xxx-STOP); or
C) the entire gene including the 5’ and 3’UTR sequences (e.g. 55555-ATG-xxx-xxx-STOP-3333)