Raj, A. et al. eLife http://dx.doi.org/10.7554/eLife.13328 (2016).
To understand a genome, one needs to know which sequences can be translated. This is particularly important in light of recent findings that some annotated noncoding RNAs do indeed encode functional peptides. High-throughput sequencing of RNA protected by ribosomes is an efficient method that allows the identification of coding sequences by the presence of a three-base-pair periodicity reflecting the genetic code. Raj et al. developed RiboHMM, a probabilistic model that takes the abundance of protected fragments as well as their periodicity into account. RiboHMM joins tools such as RiboTaper by the group of Uwe Ohler, ORF-RATER by Jonathan Weissman's team and RibORF by Kevin Struhl and colleagues. The degree to which these tools complement each other will need to be determined in a direct comparison.
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RiboHMM finds translated sequences in ribosome footprints. Nat Methods 13, 614 (2016). https://doi.org/10.1038/nmeth.3937
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DOI: https://doi.org/10.1038/nmeth.3937