Dear Friends, Hi
I have used several programs (mentioned here) for finding potentially ORF and coding ability in some of my hit-less transcripts after performing BLAST.
Intrestingly (or according to bad-luck) there were no overlap between the results of those programs.
I have heard that most of these ORF finders are based on Markov model, which is trained based on the full data set and If we run it just based on a small set of sequences, it's not going to be trained properly and your false positive ORF prediction will be high.
1- Is this really the purpose of having no overlap between the results?
2- Why Markov model is depended to input size/dataset?
3- Isn't it analyse each sequence separately?
~ Thank you in advance