Hi Ruchira,
It looks confusing to me as well, and question remain WHY? I guess it might be due to parameter differences. I will suggest you to please read this manuscript entitled "A beginner’s guide to eukaryotic genome annotation"...
I have 198,991 bp long sequence. I ran it through Maker, Glimmer and GeneMarkS. All three gave me different number of predicted genes.Here I am talking about genes that I got through GeneMarkS.Now when I am using BlastX to find the similar genes, I...