Can ribotricer infer start codon position?

[freeedog]

No description provided.

[saketkc]

Hi,

Just to elaborate on your question, you probably mean if ribotricer can detect translation initiation sites.

Ribotricer uses a collection of ORFs (defined by presence of an in-frame start and stop codons) to look for periodicity. It is possible that some of these ORFs are overlapping, and it is able to find periodicity in all of them - in which case we do not where translation was initiated.

To overcome this limitation, we require more information, for example a different inhibitor that selectively arrests initiating ribosomes [1].

I hope that answers your question. Feel free to reopen if I misunderstood your question.

[1] https://www.nature.com/articles/s41467-017-01981-8

[freeedog]

Hi,

I mean that there is some hint of where tranlation initiated even in normal Riob-seq without special inhibitor.
For example, well can tell where the translation started in the following situation, for there is no reads or no periodic reads before the second start codon: