What are gene prediction methods with high sensitivity?
Say I want to find as many protein coding genes as possible. I have valid verification approaches (whether a predicted gene is actually translated in some cell line). Thus I would want a gene prediction tool that can find as many candidates as possible, and high false positive rate is actually more desirable than low false positive rate (or: some confidence criteria can be relaxed to achieve this). Also I would prefer de novo prediction than those that need huge training dataset. Can someone name suitable tools? Thanks!
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Genes (and gene prediction tools) are very different across the different domains of life. What is your organism?
If you don't care about false positive rate could you do 6 frame translations and find all ORFs?