Hi, I used the software glimmer and online database RAST to annotate a draft genome. Both results showed that the genome does not contain some genes(here named A,B,C,D). But I used the gene and protein sequences of A,B,C,D to search(blast) the draft genome and got the complete matches. in these alignment-match areas, there are no ORFs predicted by glimmer or RAST. I was confused and didn't know how to deal with these results. Dose the genome have the genes A,B,C,D? hope to get some answers from you!
Gene prediction is not perfect and probabaly never will, if you found your gene with blast assume they are present. You can also try other gene predictors or use glimmer with a self-trained dataset to get better results.