[maker-devel] Fused gene problem, improvement in the Maker 2.27?

[Sean.Li at csiro.au]

Hi Carson,



We are currently working on the annotation of Helicoverpa genome project. Maker has been chosen as the preliminary tool for the task. By checking the annotation results by using maker 2.10, we saw some loci have the fusion problem: two separate neighbour genes are likely to be fused together and regarded as a single candidate output by maker. If we go further by looking at the outputs from each individual de novo algorithm, e.g. augustus or snap, the prediction was correct.  We are also using RNA-Seq assembly from cufflinks and some protein evidence data from closely related insects.



We noticed that the parameters "pred_flank" in maker v2.10 and "correct_est_fusion" in maker v2.27 might be useful for maker to decide when to merge models or not.  If possible, can you please explain what these two parameters can do with the predicted genes, RNA-Seq and protein evidence?



Also, our current plan is  to install maker 2.27,  train the algorithms to predict UTRs, enlarge the protein evidence datasets and input our previous annotations as model_gff. We are facing with an critical question: in which way we could effectively improve the gene fusing problem? 1) setting the pred_flank lower than 100? 2) turn the correct_est_fusion on? 3) anything else?



Thank you.



With best regards,
Xi (Sean) Li, Ph. D.

Bioinformatics Analyst, Bioinformatics Core,
CSIRO Mathematics, Informatics and Statistics
Phone: +61 2 6216 7138<tel:%2B61%202%206216%207138>
Address: GPO Box 664, Canberra, ACT 2601









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