<html><body><font face="Tahoma" size="2"><div style="font-family: Tahoma; font-size: 13px;">Hello,</div><div style="font-family: Tahoma; font-size: 13px;"><br></div><div style="font-family: Tahoma; font-size: 13px;">I am using Maker to annotate a novel, non-model plant genome. </div><div style="font-family: Tahoma; font-size: 13px;"><br></div><div style="font-family: Tahoma; font-size: 13px;">Following the published protocol, I have run one evidence-only round (est2genome, prot2genome = 1) followed by two iterative rounds, re-training Snap and Augustus each time. </div><div style="font-family: Tahoma; font-size: 13px;"><br></div><div style="font-family: Tahoma; font-size: 13px;">I have a curious result in that the gene predictors do not seem to be finding many genes, but instead creating gene fusions. As such, my evidence-only round resulted in 29,773 genes (mean length=5071 bp), and my final round yielded 29,845 genes (mean length=6530 bp). If I am interpreting this correctly, the predictors found only 72 new genes but greatly increased the mean length of all genes. I have inspected the results visually in a genome viewer and it seems that the predictors often create fusions with nearby pseudogenes. I attempted to reduce this by changing pred_flank from 200 (default) to 100, but it didn't seem to make a difference (at least for the genes I was looking at). </div><div style="font-family: Tahoma; font-size: 13px;"><br></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">So although my final Maker round looks good (~30,000 genes, 95% of genes have AED < 0.5), I have greater confidence in the models created by the evidence-only round. </span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;"><br></span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">I have two questions:</span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">1) In this case, would it be acceptable to use evidence-only gene models (from Round 1), rather than those from Round 3 (which incorporated trained gene predictors)? I ask because I haven't seen reports of Maker being used in this way.</span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">2) Do you have any suggestions to improve my ab initio training or prediction? Please note, I have already repeat-masked the genome with a species-specific repeat library.</span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;"><br></span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">Thank you for any assistance!</span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;"><br></span></font></div><div style=""><font face="Tahoma"><span style="font-size: 13px;">Kira</span></font></div></font></body></html>