Is there any existing tools for finding all uORFs (functional) across genome of an organism? I have used UTRscan and in house script for getting uORF in case of Saccharomyces cerevisiae. Is there any alternative tool for getting all uORF of an organisms from sequencing data(i.e. riboseq data)?
A database uORFs. For ribosome profiling, there are some R packages, which can be used to deal with your problem. Also referring a sORF database may be helpful as well.
Have you tried Genemark?
I believe that this is one of the finest services available nowadays
NOTE: If looking for micro ORF you need to change the setting of the program at it allows to find ORF bigger than 99 aa by default
It's a bit late reply but have you become across with ORF-RATER. Authors claim that they approach is very good for discovering small ORF's like uORFs. It utilise Riob-Seq data obtained by initiation inhibitors like Harringtonine (Harr) and lactimidomycin (LTM) in addition to CHX and non treated but works with less sensitive mode without antibiotic treated samples as well. It is described in Weissman's group paper by Fields AT et al. Mol. Cell (2015). http://www.sciencedirect.com/science/article/pii/S1097276515009053 and programs are available in the github address https://github.com/alexfields/ORF-RATER
If you use R, this one is good: https://rdrr.io/github/JokingHero/ORFik/man/findUORFs.html
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