A Question About The Gene Prediction

Question

[Ontheway]

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!

[Björn]

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.

Answer 1

[genomelover]

hi, I have used glimmer before and the output that you get is not exactly the protein sequence of the predicted genes but the gene id, reading frame for forward and backward strand ,scores and other things. I have run GLIMMER 3 on metagenomes and was stuck with this problem for 3 months. I would like u to tell me what kind of output would you expect so that I can suggest you a better gene prediction tool.